I have a GHz Pandora and tried with 1100 MHz. It only runs at ~25% speed.
The CPU frequency must be changed manually in this file...
/pandora/appdata/panmame/cpuspeed
PS: Wouldn't it be better just leave the CPU speed as it is?
The other version you mentioned was probably MAME EX (based on MAME 0.110). It probably ran faster, because MAME EX just adds lots of frameskips. I'm currently unable to try with MAME EX. It builds the games list (file seems to be correct), but for some reason, it doesn't display any games in the selection.
Frameskip can be also changed in PanMAME. Press F1 when running a game. This shows all available keys.
F11 Show FPS
F10 Throttle (auto/fix FPS)
F9 Increase frameskip
F8 Decrease frameskip
Don't know why, but I can't change frameskip in RSG. I can in Asterix, but maybe I just don't understand it properly.