I've had this issue with more than MultiCommander. An easy way to solve it is to just have a batch file or script access the mapped drives when restarting.
I use AutoHotKey for this and some other startup tasks.
There is a script called AutoHotKey.ahk which runs when AHK is started. In it I have the following...
; Try to initialize mapped folders...
DriveSpaceFree, FreeSpace, X:\
DriveSpaceFree, FreeSpace, Y:\
DriveSpaceFree, FreeSpace, Z:\
All this does is check how much space is free on each drive. It's enough to get the drives recognized. If timing is still an issue, it's very easy to insert a delay into the script.
Something similar could also be done using a standard MSDOS batch file....
dir X: >NUL:
dir Y: >NUL:
dir Z: >NUL:
I think that would accomplish the same thing.