You're right, the power supply design is different and could definitely vary in efficiency. A more even comparison might be to see what the power usage of your board is when mining at 125 MH/s. Could you test that out? I wouldn't be surprised if your design was still more efficient, but I doubt it would be 50% more so.
The design of the initial release required 5.9W at 128 MHz. (release number 110826 on
http://www.ztex.de/btcminer).
If your 1.2V voltage regulators are becoming hot (IMHO you are using two), they are at least a major part of the problem.