Yes, I have a sonnet tech ATA133. I have never heard tha there was a limit on drive size on the native ATA channel. In fact the drive works perfectly on apple hardware. Once the firmware was installed the drive worked flawlessly.
The first thing you should do is attempt to fix the permissions. To do this, launch from an OSX install disk and then select disk utility fron the file menu rather than continuing with the install. from there select your volume and then the "First Aid" tab at the top of the disk utility screen...