On closer look you're right, it's not only the arms but also the chest and around the shoulders too, and probably to a very slight degree the knees and hips. I _think_ what is happening is the Quake IV models, as they were exported, are in a certain pose, and the importer thinks it's like Doom3 and the models are still in the AF pose or some other proper rigging pose, but for whatever reason, Raven haven't done it this way for Quake IV. This would explain why the models import the way they do, the problems are most severe around the elbows, this is because the pose is the most different there too, between the ready-to-shoot pose (as they are) and the AF pose (as they should be) the skeleton expects.
Anyway, I wonder if anyone knows if the skeleton can still be used to rig custom models and export without these problems? I only assume it's the mesh problem with Quake IV imports, so the bones _should_ be okay... right?