For some people who have upgraded to Pro, they have had problems & solved them by removing all java versions & stepping back to Java 1.5;
Java 1.5 (take the JRE) & installing the "Offline" version.
As for default program, not sure what you mean. You haven't provided enough details. Are you talking about Torrents or magnet links? My guess is magnet link handler. So that means you have another program on your computer that can utilise magnet links. I had thought LW was going to stop it doing that & once you decided whether you wanted LW to use magnet links or not, then it wouldn't ask you again. But it seems you may have said yes for LW to be magnet handler, but then your other program has without telling you taken over the default handler position again. Which is not a nice way for a program to behave by changing your system settings without even asking you. This seems to be very much a windows issue. (Many programs strive to be the default program lol
)
Oh .. about your first issue with the mouse ... it's often wise to delete your LW prefs folder before you upgrade to Pro. So it might still be worth doing that. You may find it behaves better as a result.