Timer ISR firing during debugWire Flash load

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When I Debug->Restart or Debug->Start without Debugging it takes a long time for the code to load.

It will get to something like 20%, do nothing for 5 or 10 seconds, then to 50% pause a while, etc.

I noticed that the LED on the target board is still blinking once per second while this is happening. This means the timer and ISR code is running while code is being loaded via DebugWire. This surprises me.

Is this normal, or do is something messed up?

Thanks

Dave Thomas

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Should have mentioned I'm using a Dragon and Atmel Studio 6, version 6.1.2730