I received the following comment from the upstream maintainer. I'll be packaging 3.2.01 (a pre-release) soon; let me know if you want to try it.
> There are tons of TeX variants that ispell doesn't understand. > Fortunately, ispell 3.2 will have two new mechanisms that will address > the problem. The first will allow modifying the default list of > recognized TeX constructs. The second allows completely arbitrary > deformatting filters to be written as external programs.
