Here are the steps to reproduce this issue*:

(Note: By "issue," I am referring only to $window($active).logfile not returning the the entire log file as it had before. (This broke a couple of my aliases, though I suppose it would not be that difficult to work around the problem.)]

1. Install mIRC cleanly (I don't see why this is necessary)

2. Fill out your information (Fullname, Nickname, and et cetera.)

3. In Options, navigate to IRC -> Logging

4. Choose Automatically log: Both

5. Press the "Ok" button.

6. In the status window, enter:
/server irc.somenetwork.net

7. /join #TestChannel

8. In #TestChannel, type: Test 1

9. Then: //run $window($active).logfile (You should receive the entire log.)

10. Everything seems fine, at this point. Type "/run logs" and you will see the one log file for the channel.

11. Now, /part the room.

12. The log "#TestChannel.SomeNetwork.1.log" will automatically be renamed to "#TestChannel.SomeNetwork.log" when the channel window closes.

13. /join #TestChannel

14. "/run logs" will now show two logs for #TestChannel.

15. Type: Test 2

16. Manually open both logs in your log folder. One will contain "Test 1" and one will contain "Test 2".

17. //echo -a $nopath($window($active).logfile)) = #TestChannel.SomeNetwork.1.log

//echo -a $mklogfn($active) = #TestChannel.SomeNetwork.log

#TestChannel.SomeNetwork.1.log and #TestChannel.SomeNetwork.log

18. /part will combine both logs back into a single file: #TestChannel.SomeNetwork.log

I'm guessing it's related to this:

73.Fixed logfiles bug resulting in lost or corrupted logfiles when connecting to multiple servers.

So, maybe an option to disable this behavior would be sufficient.