Can Hdloader cause games to run incorectly?

I've put some imports on my HDD, and for some reason they seem to be glitchy. They seem fine at first, but on beatmania IIDX 6th style, it sometimes gets choppy during songs causing me to **** up. On DDR Extreme jap, during one song, the music fades at the same point at every time and doesn't return.
Both of these have never occured on the original disc.(my ps2 is not modded) I've played NTSC games perfectly, but I'm wondering what the cause of this problem is. Is it the HDD or what?

Hmmm...... first thing that came to my mind was the the .iso you put on the drive might be damaged or maybe the game might work on a certain mode.

Well I took the iso straight from the original dvds. They worked fine running the originals, but now they get glitchy.