How to live with noise and ground loops in a system with Electronics, Power Electronics, Electrical Machines, Three-phase power and several boards?
Grounding schemes can create problems, but not always. If you have problems with noise in your system here are two grounding configurations to check that are going to cause problems:

1) Ground loops: if you do have a shield you can make a giant loop from the shields and grounds of the devices. Sometimes its advantageous to break the shield at one end or the other to stop the currents. Another way is to use signal isolators to break the connection. It may also be possible to run the ground next to the cable and eliminate the loop that way too. 



2) Common mode noise
The other problem arises when you have a large current going through a fround that is shared by two devices. The large current will cause the resistance of the cable to create a voltage. (cables are usually under an ohm so for a 100mA current you'll get a 50mV offset from a 0.5Ω cable \$ V = I*R\$)  



To combat this don't share grounds, sometimes star topologies are better. Using lower resistance cables helps also.


If you see AC interference on lines you can block the AC currents with a clamp on ferrite bead. EMC is more of an art than a science, the reason I say this is there are so many factors and each system is different.