I appreciate all the suggestions so far. I have a few updates(and mostly bad news) surrounding this problem now.
As far as the plugin, I've tried running iTunes and Musicbee in compatibility mode, admin mode, and uninstalling iTunes. The thing that confuses me the most about this is that for my iPod Video 5.5, I was able to convert on-the-fly with no issue, and that was without the plugin. This might be unrelated, however.
On a second, more depressing note, I recently had to replace the logic board on my iPod video 5.5 due to a battery issue, and I replaced it with an identical board. As I mentioned before, I was able to sync that iPod with no issues to Musicbee, without using any driver plugin(the serial number and name would show up in MB, and the iPod would show up in file explorer as an iPod, not a hard drive. As of replacing the board, I haven't been able to get Musicbee to recognize the iPod as an iPod, and no matter how many times I've tried restoring through iTunes 9.2.1 using a downloaded firmware I haven't had any luck. I'm pretty bummed about this because it was working fine before the board was replaced, and I followed the same steps I used the first time, and now it's acting just like my 7th gen iPod classic which only reads as a hard drive. I'm pretty sure at this point I've exhausted all my options. I'm telling you this second part in hopes that you may have some insight about this bizarre bug.