I've had several problems with Melodyne/Sonar ever since X3 Producer. Haven't installed Ipswitch yet but I did continue to have problems in an earlier Splat release. Sometimes I'd get the grayed out window, other times Sonar would crash while opening a project that contained instances of Melodyne.
As far as I can gather, there was some sort of conflict between various versions of Melodyne (VST2 & VST3), so I ended up manually deleting all but the VST3 .dll from my computer, then did a re-scan. That seemed to do the trick.
I also make a habit of bouncing Melodyne-processed audio so I don't have any instances of the plugin when it's not actually in use. I still hold my breath whenever I use Melodyne simply because it's been glitchy in the past, but the steps above have been a good workaround for me at least.