Kerri Hicks emailed me and mentioned potential transfer issues with Transmits settings. It looks like the issue was not BBEdit, but Transmit was corrupting the file on upload (event though it's set to auto S/FTP). Using BBEdit's built in S/FTP worked just fine, and although Coda is built off the same Transmit engine, it seems to be without the problems.
I've submitted a bug to Panic, thank you Kerri for the direct and prompt feedback. I appreciate you addressing my concerns directly and offering thoughts on possible problems and solutions!
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