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This has been a bug since when I first started using FamiTracker but I kept forgetting to post it here.
I'm not sure if I'm clumsy or something, but every once in a while I end up pressing both the left and right buttons on the mouse at the same time. After I do this, everything I click will be held down, but won't actually do anything. Like if I click the save button, it visually gets stuck in the "pressed" state and nothing happens.
It's easy to fix as you just need to click on another window and then click back to FamiTracker, but it's sort of annoying. (It may have some lasting effects too, I'm not totally sure though...)
I tried but couldn't reproduce this bug on my computer. It sounds like a problem with some windows component, possibly MFC, so I don't think I can do anything about it other than hope it will be gone in a later version.