Chances are your strings are too thick for the nut causing them to stick. This creates tuning issues. The fact the strings don't sit properly in the nut makes this even more likely. Take it too a tech who will likely deepen/widen the slots.
im using 46/36/26/17/13/10, it was like it with the set the guitar came with. i changed them with Ernie's. same thing.
no guitar tech around here, i'll put on a set 42/32/24/16/11/9 in the mean time to see if any different