I'd be happy to do that, though I'm not sure how. It should be pretty simple to reproduce -- I simply tried exactly what eRe4s3r shows in the example above: PL_M_Body_A.GR2 and PL_F_Body_A.GR2.
I've been using Blender 2.68, but I tried the latest (2.74) just to see if it made any difference (it didn't seem to).
Basically, I used lstools to extract Main; then I put the GR2 file in the export tool folder; then I opened a command prompt and ran "TestApp GR2ToCollada" which seems to work fine; then I opened Blender and imported collada (there is only one option for import - I mostly left it blank, but I tried both ways - it seems to change the direction the model faces); everything looks good at that point - I make changes to the mesh or not to test it, but either way seems not to affect the outcome.
Then I exported back to collada, and here's where I tried every combo of option I could thing of (I mostly tried selection only with the model and/or the armature selected, and either include children or armature as appropriate). Then I tried most other options in various combinations.
When I run "TestApp ColladaToGR2" I mostly get that error, but in some cases where I only had the mesh or the armature, but not both I think, the conversion made the new GR2. Then loading that in DOS cause a crash to desktop.
I notice the new files are bigger, so maybe that's an indication of a problem.
I strongly suspect that, since it worked for you, it has something to do with what I am doing in Blender like my export settings, but I've run out of guesses...
If you could say what setting you are using that might do the trick.
Thanks for helping!