Just a guess, but maybe you were never unbanned. If you have a dynamic IP address (likely), your IP will change each time you connect to the internet. The time you got back on your IP may have fallen outside the scope of the ban. Rebooting your computer, of course, causes you to reconnect to the internet and get a new IP. This time it will fall within the scope of the ban and you're not allowed on.
It surprises me that a network should ban for a simple excess flood case, most (or at least all I've been on) just disconnect you and you can reconnect immediately. Maybe another chat with the net admins.
Something else that maybe be affecting you is "Send Queue Exceeded" error. Some scripts, on joining a channel, send a command requesting host details about every nick in the channel. In large channels on some servers the amount of data this command generates causes the send queue error and you will be disconnected. If this is the case trying connecting with a plain mIRC.
A further possibility is that you are infected with a spam trojan that attempts to send spam messages to everyone in the channel when you join, this would cause repeated excess flood errors. I refer you to google and Mentality's posts to find out how to get rid of these.