You cannot export an AAF or AFE from media being used under AMA. Once transcoded, you can export AAF and AFE. You can export an EDL as well as an XML which is done via Avid FilmScribe at this time. But just because it is XML does not mean that is just works. XML is just a description format of the tags and the metadata itself.
That is very strange and you have me stumped as well… is one setting closer than another depending on how the box is checked? And if so, is the one that is closer – how far into the file do you see it drifting by 1 frame? Is it ahead or behind?
Make sure you are selecting the proper timecode column (Start, SoundTC, AuxTC, etc.) and use Soundroll or other source as “tape” instead. Also, what version of MC/EDL Manager are you using?
Try uchecking the second box for “Do not convert sources with pull-up and down rates speed and duration will change from source” and see what happens. At the very least, the same imported file imported with either setting should show a different in duration when lined up in the timeline.