Problem solved.
I was debugging the application through LogCat and looking at the intents that were being generated by the ActivityManager. Whenever I was changing the flags of the Intent, I wouldn't see the change in LogCat. So
02-12 11:26:39.586: I/ActivityManager(766): START u0 {flg=0x1000c000 cmp=com.example.app/.controllers.Activity3 bnds=[0,153][1080,345]} from pid -1
Changing the Intent flags didn't change the flg variable in the log. Apart from this, the notification image was staying in the Status bar, my app wasn't destroying it. What I did was add the PendingIntent.FLAG_CANCEL_CURRENT
flag to the PendingIntent I was sending:
Intent intent = new Intent(this, Activity3.class);
intent.setFlags(Intent.FLAG_ACTIVITY_SINGLE_TOP);
PendingIntent pendingIntent = PendingIntent.getActivity(this, 0,
intent, PendingIntent.FLAG_CANCEL_CURRENT);
mBuilder.setContentIntent(pendingIntent);
So the problem was an incorrect PendingIntent that I must have created before, that was never being removed. Now I'm able to resume the activity by clicking the notification. Hope this helps someone that might have a similar issue.