As far as I know, the AMP's I - III were not changed for the AST mod. I know that Atrocities added a new AMP called the Genisis to the Facilities.txt, and it seems to work just fine.
What I have noticed is that if the planet is an irradated world, ie Fyron's Q mod, they do not convert.
Send me your save game file.
cncraymond@astmod.com
Thanks for the bug report. I will try and find out the cause.