I have never done as many location entries for a single record. I usually make one location entry for each set of boxes. So I cant tell if the problem has to do with the number of entries it is trying to save for one record or not.
Here is a screenshot of some locations I added to our test site for an example of how I do it:http://people.carleton.edu/~nwilson/Picture1
How essential is it that each box have its own location entry?
Couple tests you might want to try:
Can you delete a location entry from a collection you are having trouble with, and re-add it? This would make me think the record is running into some kind of limit on location entries.
Can you add locations to any other collections?
Can you add locations to an accession record? Those are stored in a separate database table from the collections, so this might tell us if the problem is with all locations, or just the collections locations table.