A simple way to tell if this is a theme issue or not...
Login to ACP
Goto Customization > Appearance > Themes
Click on Create New and choose Easy Mode.
Give it a name like "Test" or whatever you want.
Make the theme available only to your member group (like Admin)
Go to your main website and switch to using that theme.
When you have a theme that is 2 years old or older, it's going to be super difficult if not impossible for it to be automatically updated. There will be things that cannot be merged or not touched because they were previously modified. Using the method above, you will have something that is untouched in any way.
Look around and see if the problem exists there. If it does not, it's a theme problem and you need to either fix your own theme, or you need to simply apply whatever customizations you previously made to the new theme. (Once ready simply make it the default for everyone else.)
Also if you are only going to upgrade every two years, I would personally expect to be starting over with your theme when you finally get around to upgrading. You're talking about being over 20 releases behind in which there are typically MANY major changes during that time. Many sections of code across the site end up changed and if those templates are ever touched, the upgrader will ignore them so they don't overwrite anything you've done previously.