I have a fairly standard implementation of Atahualpa. The only real tweak is a CSS insert for an image background on blockquotes.
The BFA Recent Comments widget has a strange behaviour, where every few lines are not active links. Some are, some are not. I can't see the pattern. I thought maybe it was related to zebra behaviour, so I turned off 'highlighting on hover' for tables just in case, but that didn't work. I have it enabled just on category pages for testing.
The wordpress built-in Recent Comments widget works as expected. I have it on all pages for you to inspect.