Certain programs may momentarily "take over" the processor while they engage in a "major" activity.   As an example, if you have  WinPatrol, it "sniffs around" your system every few minutes (based on user configuration) for changes in startup programs, cookies, & etc.   The "sniffing" may take only a second or two, but during those seconds, you might notice a "lag" in the response of other programs... in your case, the response from your touchpad.   

 

here's what I'd suggest:  hit Ctrl-Alt-Del to open your Task Manager, click on the Processes tab, click on the CPU tab (twice, i believe) until you see the active processes sorted, in descending order, by CPU usage.  [ System Idle Process should be at/near the the of the list, using well-over 90%].  Keep this panel open, and the next time you notice your touchpad is not responding (or lagging), see what processes are running, and what has "spiked" up toward the top.

 

Hope this will help you find the culprit.