We have actually tested a very similar set up here, in house and we have never seen the errors that you are receiving. We had several 1006 (18-slot PXI chassis) connected to a Dell PowerEdge 2650 Dual Xeon via MXI-3. We tested here both without the Magma (through the single internal PCI) and through the Magma PCIx to PCI extender. We never saw the problem described so I would first say that the server software should not be too process intensive for the Data Acquisition, but we were not performing your EXACT application. One thing I would recommend is trying your application directly through the PCI slot of your server PC, this would at least eliminate the Magma hardware. Please let me know what you find from this experiment and I will be happy to assist further.
Thanks!
A. Bacak
National Instruments
Applications Engineer