I don't think it has anything to do with your hashing algorithm. I'm using MD5 hashes myself and my server accepts input from the usual suspects. You probably want to make sure you're correctly parsing your \rs and your \ns.
No, MS Windows Telnet actually displays the welcome screen correctly. You aren't sending the standard \r\n on the welcome screen, you're only sending \n. I'm going to take a wild guess that this is what's wrong with your input parser screwing up password comparisons too.
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