I have the same problem. When I mark mail as spam the log of markasjunk2 says:
Learned tokens from 0 message(s) (1 message(s) examined)
when it should say:
Learned tokens from 1 message(s) (1 message(s) examined)
I believe there is something wrong with the plugin, I think it can't read the message correctly because when the plugin marks message as junk it uses temporary file, that's what I think is the problem. I guess the correct way of doing this is to mark file as spam when it is still in the inbox and than move it to Junk folder, without checking it in "temporary" state.
If anyone comes up with idea on how to fix this let us know.