Matt
How much quieter? It could just be a consequence of the dual ganged volume control if it is only slightly quieter on one side than the other. I have gone to two, single ganged, volume controls on my Zkit1 so I can adjust each channel...what with some recordings favoring one side over the other, coupled with no balance control, I found that 2 volume controls work better for me.
Trying to find a difference in volume between the right and left channel is going to be difficult with a multimeter, difficult but not impossible. I think the best way to do it is to connect a sine wave generator (set to 1-2 volts, 1khz) to the amp input. Since I assume you don't have a sine wave generator lying around, you can do the same thing with a PC (with sound) and a tone generator software package. I looked around a bit and found this free one that looks like it should work:
http://www.world-voices.com/software/nchtone.html You will still have to come up with a cable to connect the PC's sound card line out (usually the green jack) to the Zkit1's RCA input connectors, but they are available (I even found them a couple times at the dollar store for $1, but usually you are going to pay $5-$10 for this cable). Then, with a tone going into the amp and the amp turned up loud (unplug speakers once you have things going before it drives you nuts) you should be able to compare the signal levels of the R and L channels at various parts of the amp with your multimeter set to AC volts. Be aware that your ear is a logarithmic thing. This means that a "just barley perceptible" difference in volume (3 db) is a AC voltage difference of 50% (huge AC voltage difference)...so small AC voltage differences on your meter are going to be inaudible.
Dan