I'm not sure if this has been posted before, but I for once have trouble with channels not being removed from my Perform setting.

I had like:
/join #chan1,#chan2,#chan3,#chan4,#chan5

Then I removed #chan5 so it would be:
/join #chan1,#chan2,#chan3,#chan4

Now the setting stays that way, until I start mIRC the next time. Then it's back to where it was.

make sure your mirc.ini file in your mirc directory is not read-only. (Locate the file, right click>>properties). If read-only is checked, uncheck it and click apply.

It's not read-only.

Not to insult your intelligence, but perhaps your not clicking OK, but clicking cancel instead? >:D