Queen Not Moving Up???

She's got plenty of room down below and she doesn't need to move into your third box. That is where they will store the honey for you. It's easier to inspect your lower boxes than to ask someone else what your bees are doing.

Rainy cloudy weather makes for meaner bees.

Be thankful that they're storing honey in the top and not in the lower brood boxes. If she needs more room the bees will gently nudge her upstairs. Let them do their thing and reap your rewards later.

You must have taken the MN Beekeeping class, not many people I talk to follow the 3 deep method.

I'm assuming you waited until your 2nd box had 8 of the 10 frames completely filled out. If so, your queen won't move up into that box until you get about 6 Frames filled out. Then she may move up but won't put lots of brood in that box. She may put some eggs in the bottom half of 3 - 4 frames but your middle box should be packed and your bottom should be 3/4 full of eggs and pollen. If so you are good.

When you get 8 frames built out do a full reversal by swapping out the top and bottom and leave the middle in the same location. This will move your pollen to the top for wintering. Once spring hits you will have all your pollen at the top for brood rearing.

Good luck.