Can you do the reverse, ie. get the route coordinates you travelled out of the bike GPS and map them on Google or similar? That would tell you what route your GPS thinks you took. If the route seems to be correct, then you're back to square 1. But if your GPS misses waypoints, you'll see the route cutting corners on map (resulting to shorter distance). Missing waypoints can be due to lack of signal as suggested, or it can be a "feature" to save memory space on the GPS.

Regarding your reference devices, how do you calibrate your bike computer(s)? For a 700c wheel size, a 10mm change in wheel radius means 2-3% difference in circumference. Different tyre or tyre pressure can change radius that much. If you have used bike computer manufacturer's table to get your computer set up for your tyre size, your bike comp may be several % off. In normal use it's not a big deal, at least not for everyone, but if the total difference you see is 8%, it can be significant. If you want to make sure, verify the comp setting by measuring your tyre's true circumference with roll-out method.

As mentioned before, car and motorcycle speedometers are notoriously inaccurate. They should not be used as reference. Prior to GPS, I know a few motorcyclists who installed Sigma bike comps to get more accurate speed and distance readings.

--J