If you are using specific port numbers, it may be that after the port is used and closed it will be in a TIME_WAIT state. The new version of mIRC is more precise in detecting ports that are in that state and will not use them until Windows makes them available again.
If you download a program like TcpView or CurrPorts, you will be able to see that state of each port on your system as well as their states.
If the above does not look like it is the cause, can you post a very short script that reproduces the issue for you?
