I\'m trying to run PHPDocumentor on my WAMPServer setup. It runs fine, but I\'d like to exclude certain directories, such as \\sqlbuddy\\ which don\'t contain my own code. I
You might need to change that ignore value to forward slash...
Internally, old PHP4-era PhpDocumentor still has some slash-handling of its own, where it tries to make all directory separators read as forward-slashes only. Compound this with the --ignore option values effectively being a regex mask, and it gets easy to see how a backslash (typically an escape char in regexes) can be an insidious cause of unexpected behavior.
Try using "--ignore sqlbuddy/" instead, and let us know how that goes.