Omar,
Recently I had a customer experiencing the same issue you are describing. They were using a new motherboard that supported Pentium IV processors and they were seeing intermittent failures with their PCI-4060 boards. The PCI-4060 boards would work fine in the system and sometimes they would fail after boot up not returning readings and failing the Test Resources in MAX with the error "The device is not responding to the first IRQ level", even though the board had worked previously in that same computer.
This intermittent issue was caused because the FPGA was not resetting appropriately. Some new PCs do not have deterministic control of the 5V and 3.3.V power lines in the backplane, and leave a level of voltage of a few hundreds of millivolts when powered down, which prevents the FPGA from resetting appropriately.
As you are also experiencing, they had some boards that worked fine, and some that did not. This is due to small variations in the chips themselves, and in some cases depends on the slot you install the board.
To correct this you need to send your boards for repair and reference in the problem description notes that you need to have ECO 34647 done on the board. I recommend you to send both boards for repair, to make sure you never see this failure in the board that has never shown this issue.
This is something that occurs rarely and in specific computers. Any PCI-4060 built after Nov-5-2004 already includes this fix, however your two PCI-4060 boards were built before then, even though they shipped at the end of Nov 2004.
Higher end NI Digital Multimeters (NI PXI/PCI-4070, NI PXI-4072 or NI PXI-4071) do not present this problem.
Please feel free to reply to this message if you have any questions,
Claudia L
DMM R&D
National Instruments