Hi Iiro.
I just came across this thread again while checking some things and I noticed something I missed the first time. When you do a certification completion upload, the "due date" field should be the date on which the user WAS due to complete their certification. Assuming an active period of 1 year recurring at the end/start of the year, and window of 3 months, if a user completed on 1 November 2014 then the due date in the CSV should be 31 December 2014. Totara then calculates the expiry date using the specified due date, adding one active period to it. This could also have resulted in the same behaviour you were observing. I think, to fix your situation, you need to check the due date you are providing, and also upgrade to 2.7.8 (when it comes out) which will contain the change that I discussed in my previous message (the change has already passed review and testing, so will definitely be included in 2.7.8). Hopefully there will also be a change in 2.7.8 to add some info about what the due date provided is supposed to contain.
Nathan