I also have two bikes I commute on:
Focus mares with schwalbe marathon supreme 35mm
Specialised allez conti gatorskin 25mm

The 35mm rubber is far more comfortable than 25mm but I'm ALWAYS faster on the 25mm. And I've tested over some time in varying conditions. What I found is when riding with 35mm rubber I never want to try and catch the lights as I'm just not accelerative enough. With the 25mm I at least gun for the lights and sometimes I even make it thru before light turns red.

The difference is at most 5 minutes. But... Its still 5 minutes.