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The help file from 0.3.6 works fine, but the .chm files that come with 0.3.7 and up show "navigation to the webpage was cancelled" for every page.
If the problem's not on Famitracker's end, the only other thing I can think of is that it might be Microsoft being paranoid and rejecting the .chm due to some sort of security crap (like a digital signature or something). Either way, something's up with the file that's making HTML Help choke on it.
OS is Windows 7 SP1. I'm still using 0.3.6 currently, I've been trying out 0.4.1 but still debating whether to switch for good. More than likely, however, I won't be upgrading until this issue is fixed.