Cant Save As/Upload Files

For the past couple of months I've been plagued by an issue where I can't use any functionality that requires a pop-up/modal/dialog box.

For instance, I was using Adobe InDesign, and I couldn't Save As. I had the choice of using CMD+S to save over my existing file, or close the program and lose my work.

In this situation, I used CMD+S and saved over a file I really didn't want to save over (but I also didn't want to lose my work). I then closed Adobe InDesign, re-opened it to test if the issue still persisted, and it did. Upon restarting my Mac, that fixed the issue.

This also happens in Safari and Google Chrome. When trying to upload a files anywhere, I can't simply because it requires some sort of pop-up/dialog box functionality. In this situation, I've closed/force closed every single program I have open, re-open my browser, and the issue still persists.

Just like before, restarting my machine fixes the issue. However, this is a major hindrance to my work as I keep a few browsers open and a few files that I'm working in open all week. Now I have to lose my place in everything, potentially lose work, and start all over.

I hope someone can please help!