Have to disconnect AVR STK Programer for Code to run?

Hello,

I am a total newb to hardware like this so please bear with me.

I was following the tutorials for the ATMega168 and everything was working perfectly. I had a blinking LED, I had changed the fuse bits to select a different clock divider and then later to use an external crystal (16Mhz). Then I went on in the tutorials and got my serial communication working with the MAX232 and even the shifter board kit that I purchased and put together.

One time, when attempting to program my chip avrdude reported an error about the fuse bits not matching and did I want to reset them back to what they were. One time I answered yes and one time I answered no. But after that, I could not seem to get my blinking LED to work any more.

After googling and attempting to find information on whether I had bricked the chip I came across a posting from someone (http://avrmicrocontroller.googlepages.c … rials.html)mentioning they had to disable JTAG or some such programming to work. They also mentioned that PORTC was not working because of this. Finally, they mentioned they had accidentally pulled the wire of the STK programmer that was connected to the reset pin which had caused avrdude to report errors. I disconnected my STK programmer’s wire from the reset pin and my programs are running. My question is, what does this indicate has changed about my set up? Is there a fuse bit or other config to change how PORTC works (I use the example code from the tutorials that sets DDRB and DDRC to be all outputs and then toggles the bits of PORTC and PORTB on and off to blink the LED).

Thanks in advance!