I started adding several project folders to the vault. After I added about 15 to 20 projects I started getting weirdness as I continued. As I worked at adding folders, I would click the + next to the next one to process and a check mark would be on one of the files when there shouldn't have been any check marks (the main folder check box was white). It would do it every time, one file would be select.

I also saw at one point (after the weirdness above started) where under a subfolder that I have excluded in the server, I'd select a few files in it which seemed to work but if you clicked out of it to another folder then back in - all the file checkboxes were gone but the file count remained at what it was when adding (at this point the file count was about 279).
Have you tested this with large numbers of folders, subfolders, and files??? I doesn't give me a good feeling when dealing with source code to see obvious stuff like this the first time I use it.
Exclude files list: *.; *.aps; *.bak; *.bsc; *.cfg; *.clw; *.config; *.db; *.dca; *.dll; *.exe; *.exp; *.hlp; *.idb; *.ilk; *.incr; *.lb?; *.lib; *.lk?; *.lst; *.map; *.mk?; *.ncb; *.o; *.obj; *.opt; *.org; *.pch; *.pdb; *.plg; *.res; *.sbr; *.scc; *.suo; *.user; *.vbw; *.webuser;
Exclude folders list: back; bak; bin; debug; debugmt; diskimg; dist; distfull; distr; docs; newold; notused; obj; old; release; releasemt; setup;