I have the FFXI Hard Drive, and besides the evil things it does like screw up modchips, it also breaks the Action Replay Max.
I do not use FFXI, or PlayOnline, and do not need to launch apps from the HDD (just use them for caching).
I figured it was the browser, so I went to hte HDD utility disk, and chose browser. Between 30 and 40%, I ejected the disk.
While the new browser is gone, the disk is still quite usable for HDD data saves. I'm running resident evil now, and have no problems. The modchip works too.