The problem is pretty simple, but it makes loads of things completely incorrect in the report for my website.
According to RFC 2396 (http://tools.ietf.org/html/rfc2396#appendix-C), http://example.com/foo containing a link to "?bar" means http://example.com/?bar. This is what the Site Analysis uses. This is not how browsers resolve this!
According to RFC 3986 (http://tools.ietf.org/html/rfc3986#section-5.4), which obsoletes 2396, the link "?bar" means http://example.com/foo?bar. This is what all web browsers do.
Please correct the relative URL resolution to match browser behaviour and the most current standards. (Heaven forbid you did this deliberately to match the same bug in any/all search engines.)