You will usually find this is caused by the extreme amount of users, and the impact that has both on your processor, and internet connection, which both are not concerned with mIRC.
A resolution would be simply not join channels that big, its hard to believe that 5 channels have 2000 users in it, whats that, 400 each.
If they arent chatting channels, which i suspect since your running an Xdcc script and the large number of users.. In which case, the slowdown would be caused by the warez applications posting triggers/whatnot, in which case, simply don't join them.
Also, see here