AVR-Chat

Ran into a weird problem this week while modifying the AVR Butterfly 
code for my own application.
On the Butterfly, the pins for Port B bits 4,6, and 7, plus Port E bits 
2 and 3 are used for the joystick.  I am using these pins for my own 
application and am only using the LCD driver code, the USART code, and 
the oscillator calibration code out of the original application.  The 
weird part was that all of these pins were set to inputs and I had 
pullups enabled (confirmed in Studio), but both in my application and 
in Studio's I/O panel, these bits in Port E were being read as zeroes.  
I also confirmed with a DVM that these pins were at a high level.

I got my project working by reassigning the pins in Port E to Port B, 
but I'm at a loss as to what was happening with the Port E pins.  I 
checked with the original source and the board worked fine then.

Any ideas?

Mike