Never mind, the problem was that I had an extra space inserted from the 
PHP side.
This has an extra space behind ~3,2%
$batch .= 'set datestr=%d:~6,4%%d:~0,2%%d:~3,2% '."\r\n";

It works fine now as:
$batch .= 'set datestr=%d:~6,4%%d:~0,2%%d:~3,2%'."\r\n";

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