on one of the forums I used to be on, the software was buggy like that, so if I ignored a message and then checked it a couple of days later, I'd get a -1 indicator.
I think my hitting the "ignore" button moved the inbox count to zero, and then when I opened it, it went to -1. The only way to clear it was to wait until someone sent another PM, which brought the count up to zero...
Not sure if that helps, but the email system might not like Google's swipe to ignore and counts that as opening it, or I could be totally wrong...