Way back about 4 years ago, when I was doing an application response time assessment, I also found some inconsistencies in the way that Wireshark sometimes calculated RTT. The main issue was that it didn't always correctly associate the appropriate ACK with right SEQ. I'd probably want to look at the specifics of what you are seeing to see if it was the same problem I was observing. For what it is worth, my post from 2009 is here :-
http://www.wireshark.org/lists/wireshark-users/200906/msg00068.html