RTT (Round Trip Time) calculation
The round trip time is the time required to go and return, so it must be measured from the start of the transmission to the start of the reception of the response. If you measure from the end of the packet to the end of the ACK, you are subtracting the package length and adding in the length of the acknowledgement's package (the ACK could be piggibacked on any package doing the back trip). This can very well be measured during a stream of data (and it is done so by your neighborhood TCP stack to tune timeouts and so on).