It seems that if the new sketch is going to load the "L" led will make a very quick flash followed by high speed tx, rx led action. However, when the sketch is not going to load, the "L" led flashes once followed by a pause and then the tx led will stay lit without change, and the compiler will hold at 95% progress.
As I said before, it think it has to do with timing between the DTR-reset trigger and the beginning of serial upload from the computer. I don't know how to make any alterations to that to test it however.