Large, multiway anova with unestimatable coefficients

I'm trying to run a 3 way anova with large number of levels (4x9x 10000+, with about 50K observations - it's not my data so I don't know the details). The anovan function (version 2012a) fails b/c many interaction terms have no observations and are unestimatable. It fails b/c it either runs out of memory while making the constraint matrices or (if I use less data) it comes up with infinite F values.

I can fix this by changing the anovan function,but before I do that I'm wondering if there's some other matlab anova implementation available, or if someone else has dealt with this. (Note that R can handle unestimatable coefficients, but it can't handle the large matrices.)