When I use the following line of code:

Eigen::Matrix<double,-1,-1> A;
//Fill A with some value
A = A.block(....)

I get non-deterministic results in A (what look like unallocated values with amplitudes at 1e240 or so). This also works with A.middleCols(...) and others. Is this expected behavior?

Yes, this has to be expected, this is an aliasing issue as explained there: http://eigen.tuxfamily.org/dox-devel/gr ... asing.html

Basically, in your case, A gets resized and reallocated before copying the values... Either use conservativeResize, or make a temporary A = MatrixXd(A.block(...));