I checked out that patch with Rev2 editor and oscilloscope. Psionic is right about phase cancellation being present.
There's several things I would note about that patch:
1. It is very velocity sensitive (both Filter and Amp use a lot of velocity input to drive envelopes)... so how hard you hit each key will make a huge difference in amplitude and filter character. If you want to remove that from equation, you can dial down velocity on both envelopes and compensate with higher Env Amounts, adding the same value that you take away from velocity.
2. Sync is turned on... It is interesting to note that with Osc Mix at 127 (fully osc 2), it does actually appear there is minor sonic difference with sync on/off... normally one would think the sync would only affect the sound of osc 1... Its probably a rare case to use sync if your mix is at 127, so not really an issue... but does appear there is some sort of minor osc crosstalk back to 2 with sync on.
3. Unison is on with both Detune and Slop on... so you're getting phasing from detune, plus randomness and additional phase motion from slop... this square does experience noticeable additive and subtractive interference / volume changes / phasing as the two unison voices change freq.
4. Also, several modulations targeting frequency and shapes of oscillators.
Anyways, there's a lot going on in that patch that affects amplitude and phasing. If you want to play around with Shape Mod to understand what's going on with each shape, I recommend starting with an INIT patch, and bring up an oscilloscope (there's tons of free vsts / max devices).. and just swing the shape mod while watching the scope. Also, using a spectral analyzer is helpful to understand how harmonics change with different shapes... Every different osc type and shape variation has unique harmonic partials.
I'm gonna add some info to Appendix F thread about shape mod and harmonics soon.