The Power Management settings that you refer to do not affect processor throttling on Intel processors; that is an artifact left over from the age of PPC Macs. The settings you refer to (Better Performance, Normal, Better Battery Life) now only adjust the time until screen sleep or computer sleep that you can adjust to your own custom settings. If they actually did affect processor frequencies, then what does "Custom" equate to in terms of performance? It doesn't make sense.
As far as I know, neither of your cores' operating frequencies are reduced when you switch from AC power to battery power. The Processor control panel that is part of the CHUD Developer tools shows that both cores are operating at 2.40 GHz whether my SR MBP is plugged in or working on battery. The only thing I can think of is that the frequency might be reduced when your battery starts to run low (?), but I haven't tested it myself.
Without any hard proof on either side (I can't prove that it isn't slowing down, but you can't show that it is), I'm tempted to say its just a placebo effect and that your computer either isn't slowing down or is slowing down for some unrelated reason.