If they aren't there, search your computer to see if they are being stored somewhere else. If so then there's a glitch in your registry. If appropriate files *are* in the Minisaves folder then please verify that *all* regions are being affected. Although it seems unlikely, if only some of the regions are affected then it might mean that Ubisoft has done something to deny a particular strategy I used to correct scripts. It's worth looking into.

If all the regions are affected and they aren't somewhere else then the problem is probably part of the game's difficulty with NTFS (assuming that you are using a NTFS partition). Try re-installing onto a FAT32 partition. Save your saves and minisaves to move to the new installation.