YES, it's a well known phenomena and I Don't Know Exactly Why. I do know it has to do with where the EEC "starts" from on the fuel and timing tables and that the learning process is mainly for emissions purposes, so there goes performance. My car also consistantly loses power (5-8 hp) between the first and second dyno runs...stupid computer! The rule is Cobras gain hp as they warm up (maybe due to the knock sensor's ability to maximize timing, etc) and GT's lose power as they warm up (conservative settings due to no knock sensor). Maybe if I knew why I might be able to find a way to work around this. But there are so many variables and sensor readings that the EEC takes into account and secrecy about what it does and why I don't know if we'll ever know the full story.
If there are any EEC wizards reading this, can you please enlighten us? Any info or where to go to find it would be appreciated, Thanks.