If some of the receivers and pre/pros REALLY sound different, then we have problems with the different manufacturers specifications. Plain and simple, it just can't be.
Ratpack, as others have testified, there is a rather large difference going from receiver to dedicated pre/pro. If you were to do an A/B comparison between the 990 and your Onkyo, I think you'd be shocked at the differences.
Differences between amps are rather minor, however, they are more evident between processors. But, sounds like you are happy with the Onkyo and that is great!!! Ignorance is bliss!!