If the R2 is engaged, the extra gain is left in the circuit, so your basically adding a little more gain to the lead channel when switching. The true lead channel can only be obtained with the R2 off.
I hope this answers your question. It is one of my long held peeves about the MK III switching. I love the amp, but have always wondered why they could not switch out the R2 when engaging the lead mode. Hell, it's just a relay that needs to be turned off !!!