SH3 Commander includes corrected U-boat availability dates by Flotilla. The impact is most felt in the 1st Flotilla... The IID becomes available in Sep40, the VIIC in Mar41, the VIIB in Jun41 (yes, after the VIIC) and the VIIC/41 in Jun44. The VIIC/42 never becomes available (just like real life).
Fortunately, if you're not happy with these corrections, they are adjustable/removable. Just look at the second last Q&A
here.