You may need to change the ignore value to forward the slash ...
Inside, the old PHP4-era PhpDocumentor still has some slash processing of its own, where it tries to make all directory separators only read as rewinds. Combine this with the --ignore option parameters, effectively representing a regular expression mask, and it becomes easy to see how a backslash (usually an escape char in regular expressions) can be an insidious cause of unexpected behavior.
Try using "--ignore sqlbuddy /" and let us know how this happens.
source share