Hi Monte,
it is not clear to me what really happened in your case.
What was your previous Rx buffer size?
I only can speculate that probably CDC1_App_Callback() somehow does not get called any more.
In the problem case, you might set a breakpoint in that function, and check why it does not put the characters any more into the Rx buffer.
The location is
} else if ((event_type==USB_APP_DATA_RECEIVED) && (start_transactions==TRUE)) {
So I guess either there is the wrong/no event type, or somehow the transcation is not started?
Erich