What SPI device CS is connected to D9 (or D7, D5, D6) that you are communicating with? What is the purpose?
edit: Do you have anything connected to D10 to D13? Do you have a SD card in the shield's slot? If you have a pin conflict with another device, that could cause the Arduino to malfunction. I noticed in your digital display that there is a long pause before the CS pin goes HIGH again, indicating a possible malfunction.
It's Jennic microcontroller, but it's not relevant to the problem.
I'm using pins 11 to 13 for standard SPI comm. for MOSI, MISO and CLK. All the pins that I've tried using for CS should be free and I don't see a reason why they should not work.
It's Jennic microcontroller, but it's not relevant to the problem.
Are you certain of that? Have you tried removing that microcontroller and running your digital analysis again with just the basic Arduino?
edit: The SPI function should work with no device connected. The MISO line may be floating and show weird results, but that is ok for a test. You are looking for correct outputs from the SCK and CS pins.
Are you powering your Jennic with the Arduino power?