Linux 2.6 kernel

I am facing some problems when after compiling the 2.6 kernel. The memory management or the filesystem has something wrong.
When I copy files the mouse get really slow, I can’t even start another application. I have checked many times the kernel configuration.
I have my main file system as a Kernel and the other as Modules and I have tried many combinations. Such as compiling the 2.6 kernel with the 2.4 conf.
The system is usable but, I want to find out what I have done wrong.
Would I have to recompile the xserver after the 2.6 compilation?

Prophet