Hi Costa
A board with a direct pull-up will cause the PC to try to enumerate as soon as the board is connected (powered via the USB).
This is not a problem if there is code running on the board which handles the USB connection (eg. the USB boot loader when the NV bit to start application is not programmed, or the FLASH is fully erased, or user code is available with the necessary functionality).
Where this won't work is when there is a debugger being used and the debugger must first load the program. In this case the PC will not detect the device and enumeration will fail and the only way to start again is to unplug the power, which will subsequently fail again when connected).
The same problem is true on ATMEL's EVB. The way around this is to power the board directly with 5V (external power supply), load the program with the debugger and, once it is running, connect the USB cable to the PC. Olimex's board for the SAM7X does have a switch which allows this to be controlled in SW but the header that you have is obviously made as simple as possible and so is not so suitable for USB development without a little more effort.
Regards
Mark
www.uTasker.com