Installed Rockbox two days ago. I'm having the same issue.
I have a new Sansa Clip Zip firmware 01.01.21 and installed Rockbox 3.13 using a Windows XP SP2 desktop. (I also have iPod drivers (no iTunes) installed.)
Original Firmware: USB mode set to Automatic by default. Windows recognizes the Sansa as a "Portable Media Device" without drive letter assignment. Windows Media Player will sync to Sansa (although occasionally Windows won't recognize until a reinsert).
Installing Rockbox: Must set USB mode to MSC before install. (Took a couple hours to figure that out

)
I assume above is normal.
Boot to Rockbox: Appears to be random (no common pattern I can discern), sometimes my computer will not recognize the Sansa. I must boot into the original firmware (USB has reverted back to Automatic) and must reset USB mode to MSC. Only then will Sansa/Rockbox be recognized by the computer.
This appears counter to the "The original firmware MSC setting has _no_ effect on Rockbox."
Is there a USB mode setting in Rockbox that I'm missing?
I'll continue investigation to see if I see a pattern and will let you know what I uncover. My old and flaky computer does seem to take an inordinate amount of time to assign a drive letter. At the moment, boot to original firmware/USB Mode set procedure works and is only a minor annoyance.