I'm not sure. I guess we'll need a bit more information.
Are you using VL Standard or SOHO? Is your window manager xfce, kde, or something else?
Can you describe the problem a bit more?
I think if you use HAL and xfce, you can configure what happens when you insert a cd/dvd/pendrive in Settings > Removable drives and media. I'm not sure about kde, but there should be something similar.
With VL-hot, you don't get these automatic actions (but you should get an icon on the desktop when you plug in your pendrive). So HAL we'll be a bit more automatic, if you will, at the expense of consuming more resources. If you don't mind having HAL running all the time, go for it.
Maybe you have some automatic action associated with putting on a cd in the drive, but that action doesn't pick the other drive... not sure.