Assuming the only part left here is the part with the parenthesis:
A closing parenthesis at the end is never considered to be part of the link when auto-hyperlinking URLs, because this pattern is way too common:
@Joe Turtles should be allowed to move freely (see http://freedom-of-MOVETO.com).
There may be ways to make that a little smarter, and I'm considering some, but the bottom line is:
Auto-detection of links in free text can only ever work in the 99% case.*
And since it's way more common for a link to be in parentheses than for a link to end with a parenthesis, that's what happens.
By the way, when creating manual links, we allow one level of nested parens to work with the standard case, e.g. Wikipedia or MSDN:
Check [Wikipedia](http://en.wikipedia.org/wiki/Turtle_(disambiguation)) for the different meanings.
Since your example has two levels of parentheses, this wouldn't have worked either, so you'd actually have to URL-encode. Links to URLs containing parentheses has some more on that (note though that that's in the context of full Markdown, not comments).
*We could do worse, though.