After Save As, Illustrator options window Invisible

I am working with large files that have multiple linked files. When I save as, the window pops up normally and I enter the file name I want, press ok, then normally the illustrator option window appears, you would press ok and the file saves. What happens to me is the illustrator options window sometimes does not appear. If I press enter without clicking anything the file will start to save. If I click off illustrator for whatever reason and click back, I get an exclamation sound and can’t do anything else, pressing enter won’t work either. I have to open task manager and force close illustrator. This does not happen all the time, there doesn’t seem to be any reason or pattern that I can figure out that would cause this. I can go for hours without having an issue and then it suddenly starts happening, then the window will start appearing again, or times it will start happening immediately.
I have reinstalled illustrator, updated it. I have tried having the least amount of programs running in the background. I tried it with the same files and it suddenly will work normally. I work with dual monitors and tried changing the resolution which did not help. I save on to a separate server and doesn’t seem to make a difference. Other people I work with are doing the same project do not have this issue. This has been going on for at least a year now.