Is this a common problem even with the "Arduino" standalone cards with USB programmers?
The UNO does not use the SPI bus for programming.
It uses a resident program in the Bootrom which loads the code from the UART pins (which are connected to a USB controller).
The boot program can then write the code to the remainder of the Flash memory.
You can use the same system on the Gertboard but then you have to first program the boot loader using the SPI interface
and then somehow upload the program to the UART port of the Atmega.
I think that has been done but I don't know the details.
Note that on the UNO you STILL have the same problem but then with the UART pins instead of the SPI pins.
And guess what.... They use 1K series resistors!