Jujuwar

That's a lot of new accounts posting in a short space of time... wow.

I just submit a ticket  

In the ACP > Community > Advanced Tags > Settings : disable "Add topic prefix to the page title"

What's New in Version 3.1.8
Added memory of table parameters during tag management. Fixed possible blank prefix on topic for mobile devices. Fixed schema errors on support tool. Fixed mishandling of URL encoding (spaces, etc.) in admin tools. Fixed formatting of undefined prefixes. Potential fix of MySQL 5.7 compatibility issue on tag reindex. Known issues:
Conflict with IP.Pages saving of database settings is still unresolved. Cannot provide any estimate of if or when it will be resolved.

I take a look at that and the difference is that when  Advanced Tags & Prefixes is enabled the <span> of prefix contains the template Core > Global > Prefix 
{{if $text}} <a href="{url="app=core&module=search&controller=search&tags={$encoded}" seoTemplate="tags"}" title="{lang="find_tagged_content" sprintf="$text"}" class='ipsTag_prefix'><span>{$text}</span></a> {{endif}} This template was update in .17, to add the condition {{if $text}}
And when I disable the app, the span doesn't contains this link.
This template is called in Forums > Topics > Topic at line 70
{{if $topic->prefix() OR ( $topic->canEdit() AND $topic::canTag( NULL, $topic->container() ) AND $topic::canPrefix( NULL, $topic->container() ) )}} <span {{if !$topic->prefix()}}class='ipsHide'{{endif}} {{if ( $topic->canEdit() AND $topic::canTag( NULL, $topic->container() ) AND $topic::canPrefix( NULL, $topic->container() ) )}}data-editablePrefix{{endif}}> {template="prefix" group="global" app="core" params="$topic->prefix( TRUE ), $topic->prefix()"} </span> {{endif}} In the prefix template, $text is the second parameter  
Hope this will help you!
 

@Jujuwar thank you!

@Simon Woods

I spent a while exploring it. Found the source of the error, but not a solution that doesn't break AT&P in the process. There's some really bizarre behavior going on with the IPS core here. I reached out to someone about it.

I can confirm the bug reported by @Joel R
If needed, I can provide a test site with access

Ach. Must be a side-effect of the text wrapping issue I fixed. I'll have to see if there's an alternate class/approach I can use to fix that, or something I can coopt to add a little margin back in. I'm trying really hard to avoid any actual custom styles.

Hi. After upgrading to 3.1.7, there is a space missing between the prefix and the topic title in the "topic feed" block on our sidebar. This is very minor, but with the previous version this didn't happen. See screenshot. Thank you in advance.

There was when you bought it. Removed it a while later, that change isn't retroactive though. I generated a new purchase for you.

I've published an update to resolve all of the compatibility problems I'm aware of. If you have a problem, please update. If that doesn't fix it, explain what's going on.
I do not have Pages, and I have not gotten any confirmation of whether the Pages conflict is still occurring, so that issue may still be out there. If so, I'll need access to someone's site to investigate. Last I hear, though, it may be a non-issue now.
What's New in Version 3.1.7
Fixed tag overriding prefix when the same value is added as both. Fixed style changes in IPS 4.1.13 breaking multi-word prefixes. Fixed template changes in IPS 4.1.13 breaking display of prefixes on site index. Fixed potential errors with applying prefixes from saved actions. Fixed tag/prefix changes from saved actions not updating the search index (profile, activity stream, search results). Fixed possible division-by-zero error on the tag cloud widget. Added prefix to core topic widgets. A few issues I could not reproduce:
Prefix not showing on grid view (works for me) Prefix input not displaying when creating a topic, with forum in prefix-only mode. (works for me) Homepage topic feed widget -> topic titles not linking when a prefix is present. (This must have been something custom; AT&P didn't add any such thing until, well now.) Fair warning: Most of the app will probably still work back to 4.0.0, but I will not guarantee backwards compatibility across the board anymore. It's just not worth the trouble with how frequently (and massively) things change from one release to the next. If you're running an old IPB version and you have an issue with an AT&P update, I'm going to tell you to update.

What's New in Version 3.0.8
Fixed global moderator check for the 'exclude from required prefix' setting. Fixed an empty tag if no defaults set and none entered. Fixed the default prefix setting not working as expected. Fixed a possible SQL error on some combinations of settings with the mass-add tool. Changed the mass-add tool search term field to optional. Changed the tag manager tool to only delete exact matches.

I have an update ready that should fix those issues. I'll post it when the Marketplace is fixed.
The 'updatecheck task failed' issue should be resolved now, too--no update needed for that.

Yeah. Got it, thanks.
Here: applications/advancedtagsprefixes/hooks/addPrefixToForm.php
Find: $tags = explode( ',', $container->default_tags );
Change to: $tags = array_filter( explode( ',', $container->default_tags ) );
Save, be happy. That won't fix existing ones, but you could do that easily enough from the tag manager.

As promised: Minor maintenance release for issues since July 3rd. This covers everything I'm aware of.
 
What's New in Version 3.0.7
Fixed RSS import errors with prefix. Fixed prefix disappearing on edit in some circumstances. Fixed potential cases with duplicate or empty tags.

They show up fine on VNC for me. http://i.imgur.com/sPtInHq.png
I lost my work while trying to fix my dev environment (doh!), so I had to redo all of the changes since the last update. That's done, so I'll try to test and release within a few days. Minor patch to address RSS, duplicate/empty tags, and broken prefix edit.

I took a stab at this one, but it should be fixed now.
Fixt
--
I just pushed out version 3.0.4 to fix some nagging issues. If your prefix formats didn't carry through the upgrade, you can try running the repair tool now to fix that. If there are no prefixes, it will look for old data. If you created new ones since, remove them for it to run.
Also, I came across a likely bug in the IPS 4.0 tag system affecting certain configurations. Opened a report about it here: https://community.invisionpower.com/4bugtrack/408-cant-post-tags-if-global-mode-is-closed-but-none-defined-r6780/
What's New in Version 3.0.4
Fixed forum 'defined tags' and allowed prefixes inputs not behaving well. Fixed forum 'default prefix' setting defaulting to the wrong value in some circumstances. Fixed blank tags in some circumstances. Fixed search results not linking properly if the content has a prefix. Fixed a permissions error on forum prefix selection. Fixed prefix formatting pre/post fields being required. Added a potential fix for lost data on upgrade via the repair tool.

Just released a new version 3.0.3. Should fix the issues noted above. Thanks Jujuwar. You can download it on the marketplace.
3.0.3 Changelog:
Fixed an error on forum save. Fixed an error on prefix table display, and quick search not working, in some circumstances. Fixed prefix and tag fields allowing invalid characters (", ', <, >).