Read Thread: AQ Statistics
Bonus boxes don't have locations so they won't be included in the counts, but about 15% of boxes have some sort of restriction on them. You have enough plants and finds that you should be able to see the vast majority of restricted boxes.
You'll get a few more boxes if you uncheck the box for showing only "clued" boxes--there are a few in Arizona with no listed clues that your search probably isn't catching.
But the biggest reason for the discrepancy in your numbers are series. When you run a letterbox search, it lists the series--not individual boxes. Granted, most "series" are a series of 1 so the terms are largely interchangeable, but when you get a series like Desert Drive with 5 boxes in it, it's only listed once in the search results but is still being counted as 5 boxes.
The only way to do your own letterbox count for boxes in Arizona is to go through every page of your search results and add all of the series with 2 or more boxes that you weren't counting. (In the case of Desert Drive, for instance, since there are 5 boxes in the series and you only counted it as 1, you'd need to add 4 to your running total.)
Or just let AQ do the counting for you and don't worry about it. =)
and some old boxer named AZ Roadie has done many a series