I had this issue the day the time was changed to winter one. The time for my blog was set not for a specific city ( ex. London) but according to that +2 GMT, +3 GMT system. Thus, when the time changed my blog started showing the wrong time. So, to get the right time again I changed the time in the settings and chose a specific city. Having done that I "jumped back in time" in a way and my stat numbers returned to the ones they were ah hour ago. When that hour passed I got them back.
So, I'm not sure if your changes were somehow connected to the winter time change, but I thought I'd share my idea.