That is Act Control I would guess, it's kinda like Star-Force 5 or Tages 5 (Which you've probably heard quite a bit about.) so I would assume it's part of how they integrated the copy protection with the game by protecting the core files.
Also makes the game very hard to crack or rather very time consuming to reverse as I've understood it although I imagine when a modified exe is available you could use that to access the data easier though who knows how long that could take or if a trainer from such would still be compatible with the original unmodified data, I wouldn't know since my knowledge about these things are quite limited. (It's not the ideal situation either.)
Well, currently I'm trying my hand a bit at modding the game to get some cheating done :P
EDIT: Without any real success so far. It's easy to unpack those SPK files (winrar does it). But I have no idea how to properly re-pack them, or how to get the game to ignore the SPK file and go straight for the extracted ones (deleting the SPK files doesn't work).