Okay. I have still not been able to reproduce this. Here are the exact steps I am taking:

1. Copy mirc.exe to a new, empty folder
2. Create an empty mirc.ini in this folder that contains:
[about]
portable=yes
3. Copy servers.ini to the folder
4. Run the mirc.exe
5. Enter nicknames in the Options/Connect dialog
6. Connect to a server with: /server gamesurge
7. Join channels with: //join #thisisatest1 | /join #thisisatest2
8. Connect to another server with: /server -m freenode
9. Join channels with: //join #thisisatest1 | /join #thisisatest2
10. Select first server window
11. Open several @windows with: //window -z @a | /window -z @b | /window -z @c
12. Select first server window
13. Open the @test window with: //window -znkg1 @Test
14. Right-click on Switchbar icon of @Test and select "close" to close the window

Do the above steps reproduce the issue for you?

If they do not, can you change them to reproduce the issue?