There seems to be no easy fix for this when using one chat. If you put custom chat channels in a seperate chat window that does not include the "Main" chat tab, this problem is usually avoided.
In some cases, you can setup your chat window how you like it, and save the settings to a file:
/save_uisettings myCustomFileName.ini
And then when you login, create a macro that has:
/load_uisettings myCustomFileName.ini
However, this doesn't always set the chat channels correctly 100% of the time.
I would definitely /bug it.
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