I am running some number-crunching software from the command prompt (CMD.exe). It reads a file from disk, does lots of number-crunching, then stores the result in an output file.
The program only requires around 25 MBytes of RAM during execution (around 600M is unused).
It runs much slower than it should. Both TaskManager and ProcessExplorer report that the system only allocates a small percentage of CPU time to the process (1~2%) while the "System Idle" Process remains quite high (~98%). Very little time is reported in any other process including interrupt processing (ProcessExplorer).
I have a second machine with similar parameters, but when the program is run, the OS allocates it around 30% of CPU resources (hence it runs 10~15 times faster).
Both machines are running the process at Normal thread priority. (When I increase the thread priority on the slow machine to High or even RealTime, it still only gets around 2% of CPU time).
Anyone know what might be holding things back?

Its running one core at 100% and not using the other, try running two programs at the same time or get a program that utlizes both cores. You wont really see a difference with a dual core processor until games and applications start using multiple threads. Dont worry your processor are working correctly :)