For some reason this seems to be a bug in the client, and is not related to just chaincoin, if anyone knows what the reason for this is Id love to know currently you need to do something like this, just copy and paste it into a batch file...
:loop
"C:\Program Files\Chaincoin\daemon\chaincoin-cli.exe" masternode start
timeout /t 900 /nobreak
goto :loop
RE: How to host a Chaincoin Masternode on windows.