Chris,
I am assuming you have a MXI connection from a PXI chassis to a desktop PC. If the PXI chassis is ever turned off, the only supported method to re-establish the connection is to power off both devices, power on the chassis, and then power on the PC.
The noisy fans, however, can probably be solved with the flip of a switch. There are two fan settings: Auto and High. This can be changed with a switch on the back of the chassis. I don't normally consider the 1042 disruptively loud unless the fans are on High. So, unless you need the extra cooling, setting the fan to Auto might solve both problems anyway. We also sell a 1042Q chassis... the Q stands for quiet. I hope this helps.
Best Regards,
Jeremy R.
NI - Applications Engineer