How about after I posted this question up, it completely stopped doing it....really strange. I know I recently upgraded the alternator and wiring and now I'm thinking that maybe the ecu reset itself and had to relearn everything? Pretty wierd.
Its the ecu man.... really the only way to make sure your car "sticks" to the tune is to monitor the tune and what your ecu is doing all the time.... if you ever read jbasol's thread, he mentioned how he noticed the ecu would keep trying to revert back to or near stock parameters, no matter what he adjusted in the emanage. The tune would stay for a little but, then the ecu would begin fighting with the emanage. He would have to keep readjusting the emanage to keep his tune where he wanted it.
I remember when i was running stage 2 on the stock motor with just the BB/GB for tuning. The car would run fine for awhile, then it would start hiccuping, almost stall at idle, etc. I then changed my battery (IE, disconnected and reconnected the terminals) and the car ran fine again for awhile. Put 2 and 2 together...
Unfortunetly, the best way to fix this isnt cheap. Standalone ECU and coil pack ignition. Haltech setup runs about 1600 for all the parts you need, then another grand or so in tuning the thing. I know AEM is comming out with an EMS for the evo9 that apparently works with the 3g eclipse, but that is going to be more expensive for an equivalent haltech setup. It really is like night and day switching over to a standalone with this car.