Nm, I got it myself. For those with similar problems, you need to use con2seq to turn your input/output matrices into input/output sequential vectors. No idea where you are supposed to read about this step in the documentation, and it seems like something that can be easily handled behind the scenes without having to confuse users.
These days I work with a lot of ML and AI experts, and they laugh at me for insisting on using matlab for everything. I'm starting to think they have a point.
% Instead of:
% X = num2cell(X); % X is 2x100
% T = num2cell(T); % T is 1x100
% Use:
X = con2seq(X);
T = con2seq(T);