Could it be the file is too large? What does the export file from MT look like? Is it truncated?
What I have done in the past is make my own export template in MT. Something like this: http://pastebin.com/UDAYUsPM
You'd need to change the
<MTEntries sort_order="descend" category="x">
So that you export a few at a time (above is a category at a time). You can also use something like:
<MTEntries sort_order="descend" lastn="200" offset="200">
Download them in order, a few at a time. Check the documentation on MTEntries (http://www.movabletype.org/documentation/appendices/tags/entries.html)