Delayed response to mouse commands

I have a 3 year old PC and have begun to experience
delays in the execution of certain commands initiated by
clicking the mouse. For example, when I click the "x"
box in the upper right corner of a document to close it
or when I click on an icon to open an application. The
delay lasts abour 5 seconds, during which time the mouse
arrow stays in place and the computer is unresponsive.
The only problem I have noticed is with the mouse. All
other functions appear to be normal. The extent of the
problem seems unrelated to the number of applications I
have open. I did notice, however, that the clock in the
system tray at the bottom of my monitor is running slow -
around 2 hours in a 24-hour period. When I restart the
computer the clock resets and I have no problems. Then,
the problem recurs and gets worse as time passes.

I tried closing programs running in the background and
this helped. But after rebooting, these programs come
back on and the problem eventually recurs. Could this be
contributing to the problem? If so, why now after using
the computer for almost 4 years? I recently installed a
new printer, using my USB port for the first time. Could
this be causing the problem?