As I said a wealth of different operations can modify a wallet file, but that does NOT explain your issue. Your issue is that your wallet went from hash1 to hash2 (nothing out of the ordinary), yet it went back to hash1 later on. Certain operations in Armory could result in that but the steps you describe does not include any of these.
etotheipi developed the wallet format and I did the recovery tool. We are the only 2 at Armory with lots of experience on this wallet format, and I don't expect he has a different angle on this. You should start looking at the state of your environment as well.