I haven't had a chance to try running it yet, but my first guess is the use of both alpha and root incidence.
Assuming you're controlling the twist of all the wing sections (and root incidence and alpha) then you should end up with a matrix with one row that is not linearly independent. I.e. the same effect as one degree alpha could instead be achieved by a one degree deflection of all the twist variables. You should be able to check the matrix's condition number to see if anything suspicious shows up.
I would keep alpha, but drop the root incidence. Later, you might want to set a constant value of root incidence -- but I would still keep alpha.
If you sample the load distribution at more stations than you have twist variables, you'll need to solve the system in a least squares sense. It should still work fine.
It looks like you're perturbing the twist angles by one degree (magnitude). This is a reasonable value. Although you are really building up a matrix of derivatives through finite differences, the responses should be linear and you do not need to set super tiny deflections. In fact, super tiny deflections will likely cause more problems than it solves.
Rob