When writing eigenvalues from the partial diagnolization to a text file, the eigenvalues will be truncated if the number of eigenvalues is not a multiple of 3. The file format writes 3 per line and uses integer divisor, thus causing the truncation. The function with the error starts on line 338 of HessianInt.cpp.
I fixed the problem by writing to a different file format (one eigenvalue per line). However, I do not know what would be preferable. I think a sparse format used when writing the full Hessian would be better. In this format, each line has three numbers separated by spaces: i, j, and the value. It would also be good if the eigenvectors were written in this sparse format, as well.