Unless you script yourself a logging script, this is the manner that mIRC 6.21 incorporates the logs. In fact, when you leave a channel, either by parting, quitting mIRC or being kicked, then the .1 log is supposed to be incorporated with the overall log for that channel (presuming we're talking about a channel log).
A number of people have mentioned about not liking this method, but Khaled, to my knowledge, hasn't stated if the current method is going to be the new method, or if the old method might be re-introduced as an option.
The reason for this, is so that you have current logs at all times, for all sessions. The .1 log is what records the current session, until the session ends, when it's supposed to be incorporated with the rest of the logs for that day.
I suggest you read the What's New
file, and search for logfile for more details.