I guess I should first of all clarify that Switch does not intentionally only convert part of a file in order to encourage you to buy the Plus version. There is certainly something going on here.
I did some reading on the .oma / .omg formats and I believe they are copy-protected formats, meaning you cannot directly convert these files into other formats (and I guess the fact that you couldn't convert the whole file supports this claim).
see more info in another thread here:
http://nch.invisionzone.com/index.php?showtopic=31