Our roms had the same CRC32 and I think it is the same emu, downloaded from:
http://www.filespace.org/nitsuja/mupen64-rerecording-v6-installer.exe I tried twice with a little different settings and it seemed to replay the exact same each time.
For the hotkeys here are some I have noticed that aren't obvious (not mentioned in boot camp level):
L, centers on last "action", equivalent of space in PC version
Z, acts like shift, so you can use it to set way points or select more units.
Z+L, hide/show minimap, kinda useless.
If you hold A and then load a map bookmark, it won't select units, but if you press A+Z and then do that, it will select everything in that box, so you could use this to select all your units on the map quickly, if there are less than 19.
Interestingly I don't think you can directly attack your own units/buildings in this version. Also no patrol command, not that it was that useful.