This sounds normal for a couple of reasons.
50 watt mode can easily sound louder than 100 watts, depending on other settings. First, 100 watts of output power is only 3db louder than 50 watts. I'm assuming here that your second channel is set with some dirt rather than clean, and that your first channel is clean. An overdriven preamp with two extra gain stages can easily generate more than 3db of gain. A good test would be whether the volume increases in the same channel when you go from 100 to 50 watts. The relative position of the channel masters to eachother isn't necessarily relevant -- the pots have different tapers, as ja22y said.
The LSC is a very warm-sounding amp, so the apparent volume can be tricky. I have an F-50 as well, which is much brighter, and as such sounds quite loud with the master at 8:00. I thought my LSC was pretty quiet when I first got it, because it sounded about as loud with the master closer to 10:00. Then, I ran them together, and discovered that I needed to turn the F-50's master up to 11:00 to make it as loud as the LSC. It was a bit of a revelation -- the F-50 with the master at 9:00 drowns out my whole band; another guitarist, bass, drums, 2400-watt PA, everything. I thought the amps weren't in phase at first, and I switched the LSC's loop on and off to make sure.