Okay, the preliminary results of the overly simplistic test I started are:
It appears they are using the nofollow url for discovery* at least when one link is nofollowed and one is not, but what I cannot confirm yet is if they counted the link text or PR from either... I used a unique hash for the links and have searched for both and cannot find the page using either, but the page is in the index and shows using a site: command.
If it's the case they use one and not the other as noted above I could see how results could be conflicting and there could be confusion about them, and I could also see how internal and external could be treated differently, which could also lead to some confusion, but it's not something I have tested... The test I did was overly simple, down and dirty, 'let's see what happens', but...
I'll leave it to those who would like to do further testing to do so if they feel the need, because personally I don't really care. :)
* I am doing another test to try and confirm they didn't use something else for discovery, but I'm fairly sure they used the link and will report again if it appears they used another data source some how, because that would be downright unsettling since I don't have the toolbar installed, GA on the site, or open access to stats.