[Admins]

Graal is indexing the files, it remembers the location and the timestamp, see FILENAMECACHE.txt. You can turn that off in the options, but the first start of the program will take some time then. In v4 it is displaying a window telling you that it is scanning the folders for fast access while doing it.
It can take quite some time on Windows because when accessing NTFS drives Windows loads information about access rights and such, which can take ages. It is not possible to turn off that, the only choice is to use some better file system (FAT32 is much faster, but doesn't have security options), or some better OS, or delete files. The folder scanning should not slow down the game though, it is only slowing down the start.

About lag: Try to update your drivers for gfx card and sound card, and check if you have anything running that is slowing down your computer (task manager)