SOLUTION:
This may not work for everyone, but I was having the same problem and found an easy solution.
For some reason, the session that was an issue was using the default c:/mydocs/cubasesessions/ folder as it’s project folder. The session was officially in a directory on my audio drive and the files were there as well but for some reason if I went into the audio pool it showed the ‘project folder’ as c:/
I couldn’t figure out any way to change this so I did the ‘file/ backup project’ function and saved the whole thing to a new directory. VOILA! Instant save - no problem. I’m not sure if this is because of the project folder or because saving as a backup gets rid of some extraneous crap that was causing the slow saves. Either way, it’s fixed and I’m happy. Back to making music.