Currently using InDesign CC and Mac OSX 10.9.1 (Mavericks) and server running Windows 2012, but been having issue like this for YEARS. If I launch InDesign, log in to the server and work on a file over the network, it works fine for a while. After I work on one or two InDesign files, it says I can't save the file I opened and editted because I don't have permissions. I quit InDesign, log off the server, launch InDesign, log on to the server, and can work on file, no problem. I can continue working on 2 or 3 files without problems. About the 3rd file, I usually get the permissions error. This is only working across the network. If it tells me I don't have permissions to save the file on the server, I save it to my hard drive, reopen it from my hard drive, and then save it back to the server again. Not ideal, but it's a workaround.
I have also found that I can copy or delete or rename a few files or folders from the server, but about the time I get to the third or fourth item, I get the permissions error again. (This is working directly within the OS...not from within InDesign.)
Had my IS team up my permissions to the highest level, and still having the problem...with all files but mostly InDesign files, pdf files, and folders.
I thought maybe InDesign was caching the file so you could open it from an "open recent files" menu or something, but I changed my preferences so file handling would show zero recent items, and that didn't fix it. When the IS Dept looks at the file, I have read and write permissions, but it won't let me make changes. IS can make changes. Once I log off and on, I can make changes fine.
Thought the preview might be causing this (when viewing files in columns mode, etc), but I've tried changing to icon or list view, and still get the same permissions error. Once it gives me the error, my only option is to restart InDesign and log off and back on to the server. As I said...been dealing with something like this for years, and I think it's much more than just a PDF issue.