This is easy to reproduce, type:
/echo #main,#chat
Now, move the mouse over the "#chat" part of that, you'd expect to join #chat, however mIRC joins #main. The problem is obviously due to the comma. Imho, it should work one of two ways, either join both #main and #chat, or it should detect "is the mouse over #main or is it over #chat?" it shouldn't always join #main.