I think this problem exists since 6.21.
It still remains in 6.3.
When the logs are being reloaded, mIRC will first try the last logfile available and read it, starting from the bottom, until it hits the first empty line. Then it will continue with the next logfile.
What makes the difference in re-producing this seems to be the "Lock log files" option. Disabling that will resolve the issue.