What kind of ECU did you buy? Is it the same year GSR computer, or is it chipped?
Ideally, you should use a P72 GSR ecu, but you don't have to...

You say 3500 rpms huh? If the ECU is chipped with Uberdata, and it has the launch control option enabled, there is a bug where it will not let you rev past the set-rpm for the launch control...

This happened to me a couple of times on different occasions...
Also, same thing with the CEL, it will stay lit after the car is turned "on" and then it will not flash for the codes... I had the same problem...

I bet you it's chipped and something is messed up... My problem was fixed after I re-burned the chip with my Moates.net burner...

My big question, is what ECU did you buy? A P72?