you cannot judge by looking at just one frequency, because the 303 square wave is a very special waveform
basically it "morphs" depending on frequency, and also which rapid change of frequency (for example in the begining of a new note, where the previous note was a very distant pitch)
what you hear in this wav is that the pulse width on this specific note is not equal between the two VCOs
i'm really not familiar with x0xi0 (because i am not a fan of modifying the hell out of a 303) but i can tell you, it's very easy to make the square wave sound "different" because it is a waveshaper circuit very sensitive to the parameters:
1) sawtooth bias voltage
2) sawtooth peak-to-peak voltage
3) "12V" line and C11 / R45 time constant
4) "5.333V" line and R36
there is no "right" or "wrong" here
if you take 10 303s and 10 x0xes and measure and listen to the square waves on one specific frequency you'll probably hear a small difference too
your 5.333V line should be 5.333 if you want to use CV/Gate out
you can't change the 12V line much (i think in many x0xes it's actually 11.87V, no idea about the 303s)
a bunch of months ago i made the square shaper circuit on a breadboard, then rerouted the x0x sawtooth thru it, and back into the x0x, but i used potentiometers for R45 and R36
https://www.box.com/s/26zoiu21p06763usbkqta better thing to do is to record a reference pattern which has a range of notes, including low, mid, and high pitches