My professor and chair of the department traced back a supposedly anonymus course evaluation to me. How to proceed?
Most probably nothing negative will come out of it. 

And there is also the chance that they want your opinion, independent of the evaluation (i.e., they did not necessarily guess that it is YOU who wrote these comments but given the fact that you talked to the chair about these issues, then the chair wants to discuss these with you.)

True, it shouldn't have happened the way it happened (to make you think that the evaluations are eponymous or that they have guessed the writer behind these comments and want to talk to you about that)  but most probably the chair and professor would like to discuss the issues for potential improvement. Just politely explain all these issues and make some suggestions on how they could be resolved and it should be fine.