I reported this potentially serious problem over a year ago...http://code.google.com/p/mega-isp/issues/detail?id=22
If that hasn't been fixed by now I highly doubt the AdaFruit fork is going to be merged any time soon.
On a more positive note, I have a version that has lots of goodies, including a clock output, that's about ready to be published. Unfortunately, work keeps getting in the way. It will first be published here (TinyDebugKnockBang is actually part of it)...https://github.com/Coding-Badly
If you're interested, I think GitHub has a notification mechanism (or you could just bug me once in a while).
On an even more positive note, if you are burning bootloaders, I think Nick Gammon has an OptiLoader version that outputs a clock (or maybe westfw added a clock output).