I encountered something similar when experimenting to see how much I could hex edit the stats before the game went bonkers. Then to, too much stuff running in the background, fragmented HD, etc. Have you tried running the QFI.exe in administrative mode?
sadly for this game, hex editing isnt so great
sure you can do some stuff, but they locked down most of it as said so as to not give away to much
doing the stats well since they are broke anyway kinda pointless! plus it crashes the game
buuut
all hex aside
anytime you use the sword icon on any creature before they see you, bad things happen
1.
your character if you lose and die, will lock in place and you cant move or restore or quit
2.
your character will walk north in the mines after every battle and cause crashes
3.
you character if you win the battle outside the mines will revert to WALK if you are in sneak or run
the 1st and 2nd are most important but yea no matter what attacking first seems to be bad,
also there is a timer issue where if you cast fast enough the day will never pass,
or walk back n forth between screens
I did this in prologue as sorc, got max stats on everything but climbing,
yep even thieving,
btw I dont know who did the infamy points on the wiki, but someone put ROGUE only path can rob the blacksmith, but thats not true,
sorc can do it with UNLOCK spell, simple...
just dont look in that closet... haha
suppriiise its big gay al!
jk on that last line