I am wondering whether your USB drives are booting as drive C and are then being affected by the imaging process which is trying to deploy an image to the USB stick rather than the local hard disk.
However, there are a number of bits of information missing which you should include next time you post.
First of all, are you running build 11.5.1.2266 ? Secondly, what operating system are you trying to image. Third, are your USB devices booting DOS or WinPE?
I build my own WinPE bootable USB sticks and USB drives using the technique described in this article:
Adventures with WinPE Symantec Connect
and have yet to lost the ability to boot. However, any automatic code I use for imaging, does check first that the USB device has not booted as Drive C. You can use WMI under WinPE for this purpose.