Problem solved. It turned out that SD card loaded the miso rail so I separated the miso from SD card with a 1kohm resistor. Signal from thermocouple is now correct and everything works. Thanks for any suggestions.

I checked signals on SPI bus and MISO signal is faulty if the thermocouple and the external sd card are working simultaneously. The second picture shows the correct signal when the thermocouple is working and the print goes from the internal card. It looks like the thermocouple and the sd card are transmitting at the same time.
https://drive.google.com/open?id=0BxTGGx-AlVmKdEhBdEJoVldnY3c
https://drive.google.com/open?id=0BxTGGx-AlVmKYldEdUdHbTJqdEU

I have a problem with an external sd card connected to a duet wifi board. When I run gcode from this card the thermocouple readings start to crazy and show peaks around -1900 degrees. When i run gcode from sd card on the board this problem does not occur. When I switch to thermistor the problem does not occur. The board is new and has the latest software. Did anyone have the same problem