I don't think resetting adaptations in MHD would reset the throttle adaptions?
If I reset throttle adaptation in INPA (i reset everything when I walnut blasted), you actually have to go through the throttle relearn sequence. Otherwise I got a whole load of error codes related to no adaptations stored.
I did this to relearn:
http://www.e90post.com/forums/showthread.php?t=544115
Does this issue happen on stock map?