LUNs mapped to mount points are much slower than mapped to Drive letters

Running:

Windows2003 sp1. iSCSI initiator 2.02. NetApp SnapDrive 4.1

Each night we back up mapped snapshots from our NetApp Filers on a backup
server. We had been mapping the LUNs to drive letters to do the backups,
but we have so many now we have run out of letters. Instead, we started
taking advantage of the ability in win2003 to map LUNs to mount points.

However, we took a big performance hit for this. Throughput went from 86
GB/hr to 51 GB/hr. Nothing else has changed. Switching back to drive
letters boosts performance back to 86. Now our largest job is not finishing
in the time window we have allocated. Anyone familiar with this issue? Why
is performance with mount points so much worse than drive letters?