Sadly, issues like this one are very difficult to assist with. As I understand it, the issue does not reproduce at will, but only occurs sometimes. Such problems are always much more difficult to diagnose.
The advice I can give is a boring one: uninstall SQLPrompt and see if the issue reappears nevertheless. If it does, Microsoft may be interested. If the issue disappears, well Red Gate might be.
Myself, I try to avoid to have more than one instance of SSMS open. I have some bad experience of that when I mistakenly started a second instance by a double-clicking a file, some of the settings have been lost. But that's me.