This doesn't seem to be an issue with 7200RPM drives it seems.
I guess you could put disk 1 on HDD and Disk 2 on USB
The game was built to load from DVD+HDD at the same time. Which has a higher transfer rate to Memory.
When trying to load from multiple places on the HDD the overspeed drops, and the content can't keep up with the gameplay.
All GTA games since GTA3 have had this issue in one way or another.
Just keep each disk on a seperate Disk and all should be fine.