You are right in thinking that the program is reading the specs in the spd chip. But is only running at pc100 speed.
The BIOS auto locks the spd settings to correspond with the FSB. This defaults the ram to run at the lowest setting although it is capable of much higher speeds. This is also why ram is built backward compatable.
You might try these guys and bench test that system for you.
They will run a complete analysis and (not sure) but clock the ram speed in their testing. I know they do just about every test you can think off in their analysis.
Might get lucky and it is free.