I have not personally tried either version of PwnageTool (still running 3.1.3 for regression testing), but my impression from chp1990's post at
viewtopic.php?f=3&t=164&start=10#p826 was that he did confirm those were the
major problems with each version.
Also note that there is an acceptable workaround if you do not want to use the other version of PwnageTool: simply install VoiceCentral using the Advanced option, uncheck the option to run as a standalone app, tap Install, and bookmark the resulting app instance. As long as you run it within Safari, this issue does not surface.