Difference between power on Arduino Pin 13 and Other Digital Pins
If I remember correctly, header pin 13 on Arduinos is usually connected to an on-board LED. This may cause it to behave differently under some circumstances.

The best way to understand this is to examine the circuit diagram of your specific Arduino model (or Arduino-compatible model)


Duemilanove Pin 13 LED &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Uno Rev 3 Pin 13 LED &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(marked "L")


  LED: 13. There is a built-in LED connected to digital pin 13. When the pin is HIGH value, the LED is on, when the pin is LOW, it's off.


On recent official Arduino products (Uno, Leonardo ...) it looks like the pin 13 LED is isolated by an op-amp buffer so the LED shouldn't affect use of pin 13 for other purposes? I don't know if this is the case for other companies' "compatible" products.

Notice that many (all?) of the pins have multiple alternate functions, if you have enabled those alternate functions you cannot safely use the same pins for controlling LEDs etc.

P.S. For questions like this I think you should post a circuit diagram for your added circuit (and maybe a photo too - but not instead of the circuit diagram). It is also a good idea to cut your code (sketch) down to the smallest and simplest that reliably reproduces the problem and include that code in your question.