My buffer was set to 5000 (which is standard I believe), I changed it to 50000 to try and stop this problem but it didn't make any difference.
I tried doing
//echo -s $line($active,0)
in all my channel windows and they all had between 20-200 lines in them. The amount of lines in the window didn't change by scrolling up for me, it's just the scrollbar that gets bigger and this issue I can live with, it's not a big problem imo. What I don't like is that I can't look back on conversations that have just happened in a channel
I will do a clean install of mIRC 6.31 and try that for a while and see if the problem persists.