If you are doing the SPI interface in soft, and the interrupt as it's name says interrupts the SPI comunication then, may be you exceeds the timeout of the device, then wen you return the data was lost or the rest was undefined because the device is "closed"
Why not dissable the interrups in the SPI code and re-enable after it?
If you are using C or assembler or other please tell us that at the start (i think you did not)