Alex,
Okay, I just tested this and, yes with 0.41-4 I can get the midi start/stop/continue/clock messages out.. midiin still doesn't get them, but nice, my external can be an abstraction in the newer pd instead!
Nice to know it works (and that I wasn't the only one struggling :)
In case you are interested in looking for the cause, there may be hints in the old thread I mentioned which began here.
http://lists.puredata.info/pipermail/pd-list/2008-05/062536.html
-- David Shimamoto