internal mouse problems t42 laptop,seeking tech advice

[smith07031]

Recd a t42 thinkpad today,w/out hdrive etc, Booted up fine into bios,while there, I disabled the trackpoint as I use the touchpad pointer only(mouse)
i took a working hdrive,w drivers and programs from my t40 and inserted it into t42, booted up. Everything seemed ok but I started to notice a problem. When I double clicked a file on my desktop area, I noticed that it would not open that file,rather one on the far left of it.(4 icons to left of it) Also when I placed the pointer from touchpad in start menu,there was this weird flickering like some kind of weird thing,the whole start menu was flickering on and off.
Updated mouse,and display drivers,same problem.
Finally,went into bios,and re enabled trackpoint. Right now it seems stable.
If anyone out there has ever seen or experienced this problem please post.
Of course I have tried the different settings in mouse properties in control panel.
Thank you.