Jzagaja,
Many people have complaint about the Atto not working correctly in the PowerPC G5. That could be a possible problem that the SCSI card is NOT working in your G4. I have several G4 (MMD version) so I would suggest as what Margus mentioned in his posting, try to find an Adaptec SCSI card.
I have as backup SCSI cards, Adaptec 2903, 2906, 29160, and a 39160. All of the mentioned SCSI card works in both my G4. I have an older G3 that uses an Atto card just not sure which one.
I would suggest looking on Adaptec website to find a compatible SCSI card for your G4. That would be the cheapest way to determine if its a SCSI card issue. Try to find an Adaptec card that has a return policy in the event that the problem is the same.