I was just looking into the SPI device. Do you have a capture of this? (I would like to see this). I'll run a test to see if I can cause this as well. Try pipelining that signal and if that doesn't work try debouncing using a few registers with their outputs going through an 'AND' (+ve chip select) or 'NOR' (-ve chip select) gate followed by another register (this is overkill so reduce the logic if you don't need this much debouncing).
Also are you using the function call 'alt_avalon_spi_command()' or your own implementation (for your problem it doesn't matter, I just want to know how to recreate this)?
Email me so that I can get back to you sooner.
Cheers