FF9 - strange pauses still

Alright I think this is a different problem now. I'll repeat my comp stats first:

AMD athlon 840mhz
128 SDRAM 133mhz
50x Cd-Rom (actually I'm using ISOs from HD)
10 G.B Harddrive
Voodoo3 2000 16MB 146mhz
creative labs soundblaster live value

CVGS version: 1.41
used pystek patch (otherwise FF9 won't run)
resolution: 640x480 (although during patch this is the
lowest res I can go)
used ISO: game ran from HD

Problem: I ran the game, and everything seems ok. However some spells such as Firaga, MegaFlare and a couple of others seems to cause 1-2 second pauses. Otherwise the speed is ok. Flare spell didn't have this. Is it just me or did anyone else experience this. What's the cause and what's the cure formula??
Your reply would be appreciated.
thanks
mecharmor23