I decided to take another crack at the problems I was having and Google figured out the problem.
The game messes up on a laptop that has a CPU running at variable speeds (save battery) and the game goes into "turbo mode"
The fix is adding -CPUSPEED=#### to the shortcut's program location where #### is the actual speed of your laptop processor
ie C:\DeusEx\System\DeusEx.exe -CPUSPEED=1800
So I'm now playing Deus Ex again, finished the first level just now