its a really weird problem (close the one i'm experiencing currently here even if with different behaviour.... probably a dying HD here)
The "parity" problem you got (at the beginning) should be related to the device itself and/or cabling/termination (gone now with the new cable)
The fact that HDToolbox reads the geometry wrongly the first time, it could happen.
Have you tryed to search on the net the "real" geometry of your Atlas? and type in HDToolbox manually?
I could suggest you to try with the Phase5 HD SCSIConfig but then you have to use it always.
Another suggestion.... when you install a new HD, save the RDB somewhere. If something will go wrong, you can load the RDB again and see your HD like it was prepped the first time.
Which RomUpdate do you have installed? type in a shell:
version cybppc.device FULL
Edit- ah... just for curiosity, how many "bad blocks" are reported by Q-Device with this new HD?