It assumes that Egoboo 2.8.0 or later has ran successfully. (also that it runs in the egoboo main directory)
Sooo then. If physfs isn't to blame... what is?

Code:
Initializing Win32 filesystem.
Win32 provided:
Binaries: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0
Data: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0
User Data: C:\Users\neptunium\AppData\Roaming\egoboo
Config Files: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0
Initializing physfs filesystem.
Base Dir: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0\
Warning: File not found (C:\Users\neptunium\AppData\Roaming\egoboo\import)
Warning: File not found (C:\Users\neptunium\AppData\Roaming\egoboo\remote)
Search Path: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0\
Search Path: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0\basicdat
Search Path: C:\Users\neptunium\AppData\Roaming\egoboo\modules
Search Path: C:\Users\neptunium\Desktop\egoboo\Egoboo 2.9.0\modules
Search Path: C:\Users\neptunium\AppData\Roaming\egoboo\players