TT never does the filing you do. either you go through the process to efile by clicking the orange transmit button or printing out and then mailing your return to the address in the instructions which seems like a lot of op's don't read.
regardless of how you filed for the extension, if you made a payment with it, make sure it is reflected in the return. it will be on schedule 5 line 71. some use a service other than TT for extension in which case any payment will not be reflected until you enter in the tax payment form on the line for extension payment.
there can be fees involved that have to be address before it will allow efiling. if you have a state filing requirement, efiling is not free.