Hello,
I have about a year experience with ARM and I designed some AT91SAM7x128 boards that work well but about 2 weeks ago When I completed assembly of a new board. I found very strange problems that I couldn't solve till now.
I use ULink2 and Keil uVision IDE to program/debug the chips.

Main Symptom:
When I Assemble the board and make sure all voltages are OK I try to connect via uLink2( to download the code or erase the flash) but I get the message
"Could not stop ARM device! Please check the JTAG Cable"

Jtag is OK
Jtag is ok because it works with other AT91SAM7x128 boards also firmware is the same. even schematics used for ARM MCU part of new board is the same as old working boards. only PCB Layout is different.
I think I have Jtag connection because Oscilloscope shows activity on all Jtag lines and uVision can successfully get Chip ID in uLink ARM Target Driver Setup as 0x3F0F0F0F.
Also I lowered the Jtag Speed to 100K but still no progress.

NRST loses its Pull-Up
One of strange symptoms is that at first I have about 3V pullup voltage on NRST pin. VDDin is 3.39V and VDDout(Core Voltage) is about 1.85V. To Resolve the issue I did what I read in the tech support article of keil
http://www.keil.com/support/docs/3215.htm
i.e. I tie NRST pin to GND and power up the chip, after about 30-50 times of doing this I found that NRST pin lost its pullup and after power up remains float(tri-State i.e. High Impedance). I have changed about 4 chips and all had the same fate but even new chips that still have their pull up resistor(3V after power up) behave exactly the same as chips that have lost their pull up i.e. Ulink can't connect to them ?

Reset Signal of Ulink in Chips that have pull-up
When I probe Reset Signal of Jtag with oscilloscope, I see that after I send Erase Flash/ download commands the reset signal(NRST pin Voltage) goes low and remains low until IDE gives me the message that "Could not stop ARM device" and only when I click ok on the message box and message box goes away, reset signal again becomes high.

Thank you

Have you checked the external oscillator?