The Matlab documentation seems unclear about how to ignore missing data when using kruskalwallis, the Kruskal-Wallis (or any other related) test. The same goes for unequal group size.
Very late answer, but I ran into the same problem myself today, might as well help some future searcher.
The solution is pretty straightforward. kruskalwallis is primarily used on matrices and by default compares equal-sized columns, but it does allow you to instead assign groups manually, with the optional variable "group". I was attempting to check whether a single value was unlikely to belong to a distribution from a different set, so this was straightforward. I just added the value I wanted to test on to the end of the set I was testing against, then made "group" a vector of ones the same size as the set, with a "2" added to the end for the new value. Looks like it worked quite nicely.