I was on IRC for a bit this morning, and I brought this issue up.
It was suggested that the pauses are actually related to the SD card.
<torpor> it doesn't happen for me when i'm using my panasonic card, but when i use toshiba, i occasionally see these lags..
Squidge mentioned that the GP2X does not mount the SD with "noatime" so at some point, the OS will start marking the file access times on the SD card. Anyway, I tried unmounting my SD and then re-mounting it with the "noatime" option. It seemed to help the pausing issue. There were still some small pauses, but they weren't nearly as long or noticable.
I logged in via USB Serial Gadget and ran this.
"mount -t vfat -o remount,noatime,nodiratime /dev/discs/disc0/part1 /mnt/sd"
Then I re-tried my game. There were still pauses, but they didn't seem to come along as often, and they were definitely shorter (like maybe a fifth as long).
So, that's the data for now. If you notice pauses, try another SD card, and please let us know if that (or anything else) helps.