They've started doing shady things like bundling adware with "abandoned" projects and making it difficult for projects to leave. They've also slowly been pushing more and more advertising and "fake download links" (the sort of things that look like a download link for the project but are actually an advertisement of some kind) for the past few years.
Their behavior has become questionable enough that it wouldn't entirely surprise me if they were partly the problem, although I'd be a bit surprised that they would just corrupt an upload to their site.
Since the checksums clearly don't match, an alternative download link would probably help debug the problem, yeah. Perhaps Mega? I used to use WePlayCiv's download section as an alternate to CFC for files that were larger than the size limit here too.
Thanks TC01 I'll look into them this weekend.