I, too, am having this problem.  I have tried all of the above suggestions to no avail.  If after I "start debug" the second time, I close the IDE and start PuTTY on COM3, and then press enter, the application starts running and the serial data appears as expected.

I added the following code to the application:

unsigned strokes = 0, rest = REST, firstTimeSwitch = 1;

void firstTimeBreakpoint()
{
     firstTimeSwitch = 0;
     Serial.println("first time break point");
}

I call this function as the last thing in the loop() function, as follows:

if (firstTimeSwitch)
           firstTimeBreakpoint();

I set only one breakpoint, on the println line.

If I initialize firstTimeSwitch as 0, firstTimeBreakpoint, is never called, if initialized as 1, it get called only on the first pass through loop().

So, if I :

1) reset the IDE
2) initialize firstTimeSwitch as 1
3) "start debug'
4) "STOP DEBUG"
5) "start debug" a second time

the application runs through the loop() function once and hangs.

If, on the other hand, I:

1) reset the IDE
2) initialize firstTimeSwitch as 0
3) "start debug'
4) "STOP DEBUG"
5) "start debug" a second time

The application runs as expected, but, the serial data does not show up on the serial monitor.  I can stop and start debugging as many times as I like but the serial data is missing.  If I "unclick" connect on the serial monitor and then start PuTTY the application is restarted and the serial data is present.  If I then close PuTTY and click "connect" on the serial monitor, it won't connect, the connect box becomes unclicked.

I have never had this problem before today and it is present on all applications I have tried.