snehapshi...@gmail.com wrote:

Do not run the timer on the Event Dispatch Thread (EDT).

Study Swing concurrency, hard, starting here:
<http://java.sun.com/docs/books/tutorial/uiswing/concurrency/index.html>

I hypothesize, absent sufficient information from you, that your starting
thread is waiting for the timer, and that you start it from a GUI event
handler, thus awaiting the timer in the EDT.  Nothing else can happen in the
GUI until each action completes, in this case the wait for the time to expire.
 You have to start the timer in a separate, worker thread, and have the
worker thread update the GUI upon completion through invokeLater().

Of course, no one can help you with confidence until you actually tell us what
the problem is.  You have described the overall picture, but given us no hard
data until you provide an example - a simple, self-contained compilable
example of source that evinces your problem.
<http://mindprod.com/jgloss/sscce.html>

Without that we're just pissing in the dark.