Playing around with the convergence criteria again didn't lead anywhere and I couldn't spot the difference between the two sets of code (ours and the the other JAMA port). Reading some comments on HQR2 suggest that there are just some matrices that it doesn't work with but I couldn't figure out what conditions cause it to fail.
MKL seems to handle the 650 matrix fine (and was quite quick). I'll add the LAPACK routine geev to the native wrapper and perhaps that will work for you.
MKL seems to handle the 650 matrix fine (and was quite quick). I'll add the LAPACK routine geev to the native wrapper and perhaps that will work for you.