That is hard to believe as the audio channels are discreet in the soundtrack and the processing.
It is possible that chaos83 is unknowingly using some sort of DSP mode to alter the sound, but otherwise, yes, it seems unlikely that there would actually be an audible difference in channel separation with discrete multichannel sources.
chaos83, what source is it that sounds "more ambiguous" with the Yamaha? If it is a DVD, are you outputting the exact same soundtrack from your player? What processing modes are engaged? If you want it to sound as it was intended to sound, you must not engage any extra processing of the signal; you would just want to engage the proper decoder for whatever is input into it. And, of course, if you are comparing between two receivers, if you used a special processing mode on one that you did not use on the other, then that can explain why they would not sound the same, which has nothing to do with the quality of the receiver. Also, if the Onkyo had the channel balance incorrectly set, it may sound different from having the channel balance right. Some people willfully turn up surround channels or the center channel higher than other channels, though I do not recommend this.
Also, if you moved the speakers between using the different receivers, or moved your seating position or furniture significantly, it may sound different.
Another possibility is suggested by bandphan, as some automatic setup systems EQ the speakers in some way or other, and that can affect how it sounds as well. If one used an EQ, but not the other, then two receivers may sound different due to that.