Bad update on tune?

[hydrasport]

ECM failed a few weeks ago. Was able to remove the 93 diablo tune and then have car towed to local dealer for new ecm. Car ran fine for the first few days while trying to relearn fuel trims and transmission shifts on factory stock tune. Updated the diablo I1000 and reinstalled the 93 tune. I chose the firm transmission shifts and modified the fan temps to go with the 160 stat. The car did not idle well and had stalling issues after long runs on the interstate. It also had a surge that was never there in the original 93 tune. I replaced the plugs and wires just as a simple check to make sure the old failing ECM didn't cause fowling. Last night the idle dropped below 500 while idling along in a parking garage. It has a flatspot in low speed acceleration. Today I removed the 93 tune after a few logs in the shop. The factory stock tune seems to run much better and has better idle and acceleration.
Is it possible that the new update to the 93 tune has an issue?

[mikel]

have you tried updating the tool in between?