First test: is controlling the pinout of the transistor
Second test: controlling it is correctly wired.

If you have wired as in your drawing, connecting the base of a NPN to ground had never made flowing current through the collector. So either the transistor is defective or it is uncorrectly wired.

I think it is an issue with the driver and windows 2000. Windows 2000 is more restrictive on the way you access the hardware and the drivers should gain some privilege to execute.

Is there any windows 2000 guru here to confirm

wich eee is it?
Wich OS do you run?

In ATmega datasheet it is said that SS pin is only used while the processor is in slave mode. In that case when SS is driven low by an external master it puts MISO and SCLK in high Z. When the ATmega acts as a master there is no automatic management of the SS pin and the software manages the SS pin itself or any other one used as a Slave Select

But my problem is how to brake the motor

The motor controller has no braking function. And when you put to neutral the motor is floatting.

placing it on reverse while going forward is not advisable for my motor controller.

Why? It is just EMF vs back-EMF. Of course you should not go from all forward to all backward. But if you slow down the motor and then put a little reverse I think this will brake the motor.

If you use the led blinking circuit it will show you that there is power but not that the arduino is still alive.
To know if the arduino is alive you should blink the led with the arduino itself.
To do that you can put the atMega in sleep mode and program a timer to wake it up blink the led and return to sleep. If the ratio of the time it is alive versus the time it is sleeping is really short the consumption will be negligible.

arduino duemilanove with [glow]atmega328[/glow]

I'm not sure this configuration was supported in arduino 13?
Why don't you use a more up to date version of the IDE?

Not only the voltage is of importance but the frequency too.
Double check what is specified on your power supply a bad frequency can lead to many smoke

To switch between potentiometers that are analog pieces, you should use an analog multiplexer like 4051 for example.
Look here for an explanation http://www.arduino.cc/playground/Learning/4051

did you select the right serial port and the right board in the tools menu?

USB don't deliver an accurate 5V. It is 5 +/- 5%

Are you using an FTDI cable to download?

- If yes is the driver installed

- If no, you are probably using a com port. So are you sure TX and RX of computer are connected to the right pins on Ardweeny. This is a common mistake with com ports.

Have you selected the right board on the Tools menu of the IDE?

Which OS?
Which IDE version?

we miss many information to help you

What kind of audio circuit?
What audio chip?
How do you plan to control them?

and so on ...

Both cards are the same.
The 20PU means
20 for 20MHz version
P plastic DIP package
U lead free