Just installed Notepad++ 6.4.5 (UNICODE) Build time : Aug 9 2013 - 17:33:38 on my Windows 7 Pro x64 machine. Microsoft/Windows Update shows no updates available, so I think I am current, as of today.
I use a SUBST'd drive when I work on projects I brought home from work so that all of the project references match. Notepad++ says that the SUBST'd drive does not exist. If I copy the fully qualified file name that NPP says does not exist into the File Open box for Windows Notepad (or anything else) then the file opens up fine. (I've also noticed that the drive/folder listings for the Default and Custom Backup directories also refuse to admit the existence of a SUBST'd drive, and since they use a different interface that the File Open dialog, this appears to be an INTENTIONALLY CREATED issue.)
Not sure WHY NPP is singling out SUBST'd drives for exclusion, but IMHO it is a BAD thing to do. Is there any hope that it will be fixed?