I followed the steps you described and was unable to reproduce the issue unfortunately.
The routine that processes channel joins in 6.2 is identical to the one in 6.16. There have been no changes to it since 6.16.
Have you tried testing this with a clean copy of mIRC, by copying mirc.exe to an empy folder, with no other copies of mIRC running?
Are you able to reproduce this issue with a simple "/timer 1 5 /window @test" ? Or does it only happen with "/timer 1 5 /hop #"?
