So this turned out to be a bug in my own code after I made the original change in trilinos_sparse_matrix.cc. When I was constructing the sparsity patterns for the matrices using DoFTools::make_sparsity_pattern, there is a flag I had set keep_constrained_dofs = false. Setting this flag to true has fixed my matrix multiplication problem in parallel (though it's not really clear to me why this would only cause a problem in parallel).
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