You are exactly right... I had clients that paper filed the 990 return before it  was  required to be efiled, and they also received irs letters that they didn't file, but the certified mail receipt looks like it took care of the matter.. other CPAs on this forum also had the same issue.... this year the software would not let me electronically file the 990 extensions.. So what did I do? I just hurried up and finished the actual 990 returns before the due date and electronically filed them, i.e. no 990 extensions.... we should not be experiencing this nonsense, plain and simple..... just my humble opinion...