This is a run down of my personal glitches with the collada exporters in Blender. Your builds may not have the same problems, but I had to stumble around in the dark to find the ways around mine, so if these issues are plaguing you too, might be worth a try. This is not telling you how to export in Blender, or how to use Blender, it assumes you know that already- just that you are having these particular export glitches when doing it.
I primarily use Blender 2.49 (an old Jass build, that's long since not been available for download. It's comfortable for me, it predates Primstar, and it doesn't have some of the other glitches/intentional refusing to do what I want that was introduced that messed up my workflow). I haven't really jumped on the 2.5 bandwagon much yet, 2.49 does what I want, how I want it, and I haven't spent the time to find the way to work around 2.5 (just trying to cam around in it irks me with the new settings, and I haven't spent the time to get used to it or change it!)
Around half the time, exporting with the collada 1.4 exporter works just fine. The other half...it randomly divides out a few faces and assigns them to new texture space (the closest to tracking down any reason behind which faces it chooses I've come to is that sometimes, but only sometimes, when I merge edges, it glitches some of the faces to one side into a new texture space). This is NOT visible in Blender- it assigns texture faces just as you would expect, you only find out when uploading the collada and either the uploader fails because your models do not all have the same texture faces (or have too many- also note that you actually have to have all the _same_ textures assigned, not just the same number as well- or at least I do!), or you get it uploaded and find out you've got some straggler faces sprinkled around here and there that have a different texture face.
I've tried all sorts of ridiculous and time consuming experimentation with trying to track those down, fix them, replaced my collada exporting scripts with new versions, all to no avail. Finally I found one thing that actually fixed it: opening that blend file in Blender 2.5, and exporting in there.
BUT. The collada exporter in Blender 2.5 is twitchier. You MUST always make sure to tick the "export only selected" box in the file popup or it will export your entire blender scene with all pages in one piece (with my workflow, extra pages have the other LODs and collision and in progress working bits, so it's an enormous mess). ADDITIONALLY. IT ONLY SOMETIMES DOES NOT EXPORT THE UNSELECTED THINGS ANYWAY. This last go round, it would export around half of the rest of the stuff that had nothing to do with what I wanted to export, even though it wasn't selected! It was a consistent half, but it was not a helpful half.
So, time for making a copy of your blend file so you don't save over and lose everything. Open that in Blender 2.5. Delete everything on ALL the other pages. Delete everything you DO NOT NEED on the page with what you want to export. IF YOU ARE EXPORTING RIGGED MESH, DO NOT DELETE THE SKELETON. It needs that for the skeleton data. The body you're building around? All that can go, but not the skeleton itself. (And make sure it's the right skeleton if you've duplicated things for alternate working versions, of course.)
Last note: current version of the SL mesh uploader seems to require the collision object to have the same number of texture faces (and the same textures!) assigned as the LODs. Previous versions of the uploader did not, future versions may not again. There is no reason for collision to require textures assigned, and there is no helpful red error message, the button to calculate and upload just silently disables itself.