There is also one more area to check, although this probably isnt the case in this particular situation. Look at the entries in the third icon from the left, on your toolbar. Although this comes 'pre-loaded' with a lot of default channels to join, it's possible to make your own list, and even automatically join them. This option is available on a 'per irc network' basis, or all networks.
Hope that this helps,
Listner