This problem I had was driving me crazy, then I snapped to the logic, that the two boards must present the slots to each other straight, even if there is a small curve in the boards.
Once I got them together, I could bottom the fingers in the slots with clamps, at times every clamp I have.
Another problem I run into was, wood glue dries to fast, or I am too slow getting the box togeher, square, and all the fingers bottomed- "more then 40 on a corner". Its much easier the wider and fewer slots, but I like the looks of narrow slots.
I found using a slow cure epoxy glue made it much easier to get the work together.