That's most probably because of the difference between the time on your N9 and your cell operator, and nothing to do with FasterN9.

I've got the same thing. My N9 clock is about 5 minutes faster than my operator's time, so if I get an incoming message at, say, 13:25, the timestamp on the message will actually say 13:20 (which is the operator's time).

If I reply to this message immediately, the timestamp on the outgoing message will be 13:25 (N9 time). So far so good. But if the other person replies immediately, then their timestamp will be around 13:20 or 13:21 (operator time).

Hence my message, and not the latest reply, will have the newest timestamp and will show up in the inbox pane. Hope that makes sense.