We are running PS CC2015, AI CC2015 and inDesign CC2015. We are on PCs and work strictly off a server. We used to run Macs, but even on the Macs, we started noticing that files were not saving to the same location that they were originally opened. This has resulted in files being saved all over our server and job being incorrectly printed because the last file that was in the actual "folder" was being used as opposed to the last revised file which was saved in some other location. We were told by our IT department that it was because we were on Macs and when we upgraded to Mountain Lion, that caused the problem (we didn't have the problem when we were running CS6) and we were also told it was because of our server being PC based (EMI VNXE3200 is the server) and us being Macs. So, we started over, got rid of all of our Macs and got PCs, but the problem still exists. We often have multiple files open at one time so when we just hit ctrl+s, we think we are saving to the same location. I have read that using shortcuts and the "recent places" can throw off the directories. Also, does the way we name the files have any influence on this? Could our server not be configured correctly? I have been recruited by my manager to figure out a solution to this and really need to figure it out quickly before we really have a major, major issue.
This is a past discussion, for a different program, but I think the idea will be the same for what you are using... not DESIGNED to do what you want, so may or may not work
Premiere Pro does not work properly, if at all, over a network - https://forums.adobe.com/thread/1835472