I have been having problems with the scroll wheel in a couple applications for months now and I've only just recently put the pieces together. The two apps in question are HexChat (IRC client) and Deluge (torrent client). Both utilize GTK for the UI. With Deluge enabled, neither are able to reliably utilize the scroll wheel. Other applications are not impacted. As soon as I disable S+ scroll works fine in these apps.
In the interim it would be OK if S+simply ignored these applications. I have set them up in the "Ignored" list. If I select "Disable S+" S+ does in fact disable itself when the selected applications are activated. The trouble is that it doesn't turn itself back on when I switch to Chrome or whatever. Is this expected behavior? Is there some way to let S+ simply ignore these applications but still be activated when other applications are running?
Some details: OS: Windows 8.1u1 StrokesPlus: 2.8.2.0 HexChat: 2.10.0 Deluge: 1.3.7
Have you tried unchecking Keep Gesture Draw Window On Top* and Don't Hide Gesture Draw Window*? Not sure if that's the type of problem you're having or not, but worth a shot at first. Also, do you have Allow Mouse Wheel Tick* checked?
Glad to hear! Yes, some of those apps see there's a window, even though transparent, above them and choose to assume they don't have focus, thus don't respond to normal events... Or something along those lines.