I have been running a slightly modified Madwolf tune on my car for a while now. Car has been running fine. There were a few things that I wanted to change though.

I wanted to:
Disable DCFO (decel fuel cutoff) to be nicer to the vacuum controlled transmission
Remove the stock rev limiter since my ignition box has one
Increase the commanded AFR for cat over temp since I don't have cats.
Lean open loop some more
Increase the amount of throttle for WOT (due to the 3000 RPM converter)
Make sure the EGR system is disabled, not just codes turned off
Turn the Misfire test back on (just testing this one).

So I took the tune that had been working for me, and made the above changes to it and loaded it to the car.

The next day, I noticed that the car wasn't cruising at 14.7:1 in closed loop, it was cruising at 14.5:1. Then after stopping somewhere and then re-starting the car, it ran at 14:1 on the drive home. Also noticed that while cruising along, the converter would occasionally unlock and wouldn't lock back up, until I pressed the brake, then drove a couple minutes more.

Contacted Dynojet about the WBO2 sensor's life span, they tell me that it should last up to 100k miles depending on it's use. In the case of my use, they tell me slightly shortened lifespan due to the nitrous use, but it should still last a good while anyway.

ASSuming the car was just having to "learn' the fuel trims again, I made another adjustment to the tune, the fan temps. I upped them slightly so the coolant would be slightly warmer for heat this winter. Car exhibited the same cruising AFRs.

Yesterday I adjusted the shift points trying to tackle the 1-2-1-2 shift shuffle that the car's been doing. I took the car out and logged it. The car was running about 13:1 in open loop, and after a couple minutes it went to 14:1 in closed loop. When I started driving the car it went to 14.5:1 while driving, but it idled at 14:1.

I drove into town, got out of the car to pay a bill (left it idling) and drove back out to pick up my son from school. I ended up behind a slow truck, so when I got room, I punched it and took off. Run up to about 100 or so, then got out of it. I looked over at the laptop, and the car was in OL again. It never did go back to closed loop, either. When I got to my son's school, I stopped the log, and checked for codes. I got a couple of o2 sensor codes.

Last night, before going to bed, I stepped back to the tune before I made all the above changes. Fired the car up, it idled at 13.5:1 in OL, then 90 seconds later it went to CL and idled at 14.7:1, just like it used to.

The changes that I made to the tune should not have had an effect on the normal AFR in closed loop, or at least I wouldn't think they would. So my only guess is that there was a problem with the tune file itself, like maybe it was partially corrupt or something.

Now that I'm back with what appears (still need to drive it a bit more and verify) to be a good tune, I will make the changes I need to make, but I'll do it just one change at a time until I see what caused it in the first place.

Has anyone else ever seen this happen before?