Having spent my whole working life in non-profits, I agree with everything paulina said, and add one more thing to consider. Funding has been drastically reduced to almost all charity organizations nationwide and perhaps this one has had to lay off staff. Maybe they no longer have the person who was responsible for donation acknowledgement and haven't fully adapted to fill that void yet.
Since you did send the package with tracking info and then failed to actually use that info to follow up as soon as it was apparent they should have been received, you have only yourself to blame for any worry you went through. Yes, the organization should say 'thank you' for your donation (and in fact should be sending written receipts for all donations for the donors tax returns), that's NPO 101, but their given reason is no less flakey than the one you gave for not meeting the promised deadline.
