I have an atmel 328 running a Due bootloader. I am using a communications chip to convert RS422 Serial into TTL serial to communicate with the arduino chip. I am able to upload the code to the chip using an UNO as an ISP. I have wires coming off the TTL lines such that I can watch the stuff going by too, and can "talk" to the arduino Due chip.
If I break the trace coming out of the communications chip (level shifter) to the Arduino Due Rx pin, then my Due runs well, responds to TTL input, and my LED blinks like I want it to (100ms delay). When I use a board with the level shifter to Rx line intact, the blinking code has about a 1500ms delay (where I asked for 100) and it won't "talk" on the Serial Tx line when I upload a program that just spews out characters.
I get the sense that the level shifter is doing something to the Rx pin on the arduino Due and causing it to pause and think a lot. The whole board will power up too when I plug in the TTL Tx and Rx lines, making me think that they are pulled up on the Arduino and the level shifter.
Any insight would be greatly appreciated!