Thanks for your report.
Those bugs have been partially solved in last beta.
https://dl.dropboxusercontent.com/u/13064071/plantuml.jar
The issue that remains is: how to connect some note to a "if" or a "fork" ?
We are looking for a nice way of connecting the note to either the starting diamond of the "if",
the ending diamond of the "if" or the synchronized black bar of a "fork".
It's both a question about graphical design and about our internal Java code design.
So we're still working on the question...
Regards,