I've created a pull request months ago tackling this issue: https://github.com/q2a/question2answer/pull/39 (Also related to question http://www.question2answer.org/qa/29015)
The final code was modified by Scott and is this one: https://github.com/q2a/question2answer/commit/786b0322159ca2023c6f570f0a9b49054a754771
This means if you replace the content of function qa_html_convert_urls in file qa-include/qa-app-format.php with the one in the previous link then it should work. Anyway, note it is not magic, it is just a guess on how URLs should end as, technically, anything after an HTTP:// could be part of the url.
As this has been added to 1.7 then you could just wait for that release or replace the function and then, when the new version is released just copy paste the file as that function will behave the same.
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