We have been receiving emails with regards to Hardware limitations with SPI. We are currently looking into contributing to the open-source SPI driver to work around the hardware limitations in hopes of fixing or at least improving this situation. However, we cannot promise the full resolution of the problem.
So far, we've tried fully disabling Full-Duplex transmissions, however, this still causes data corruption in Half-Duplex transmissions.
It's important to note that software-based SPI (bit-bang) can be setup on the Omega. It will have an upper limit in speed (about 1MHz clock frequency) but the data will be valid.