Having this issue some times aswell. Mostly it works flawlessly for me.
You can always contact their support. They usually answer pretty quickly and really try to improve your situation.
Oh and I heard that sometimes the automatic API import still messes up a little bit with some of the exchanges. How much are your stats off?
I switched to paid and got API imports setup and found that some of the dummy fee balancing transactions I entered manually in the past with my free account were no longer needed and now everything is balanced out. Loving it.
Glad to hear that everything is working out fine now :)