"Aggregate storage applications ignore update to derived cells. [2.20705e 006] cells skipped"
Looks like you are loading more than just level 0 data.
"I ran an aggregation after the data load, but when I try to retrieve data from the new cube, I get all zeroes."
All zeroes? or #Missing? If you are seeing zeroes, you are either loading them or you have it masked in your add-in options.