I don't do too much importing/exporting of files, so I can't help you too much, but I'd like to ask a few questions I hope will at least be able to help nudge us both in a helpful direction (you, being helped; me, understanding).

Anyway...:

1) You modeled/rigged in Maya, aye?

2) Is the program you're trying to import the file INTO able to understand Maya's Rigging information? Do you know if it can/can't?

and lastly:

3) Do .obj files contain rigging information, or only geometry information?

I know that computers work on a deeper level, but knowing that .obj essentially means "object (file type)," I'm curious as to if a .obj file only contains geometry information, or any/all information like rigging (thus my question :p).

If, ultimately, .obj's continues to not work, are there other file types you can export/import as, so see if those work instead?

EDIT:

p.s., always save before trying something new; keep backup files