Hi, You have a lot of stuff running there.
Tell us more about the different power sources and how the grounding/common of the power/relay parts is done.
If you are using SSR's you should have complete optical isolation for the power section. Can you confirm that Arduino ground is NOT connected to the power section at all?
Some information about these problems is here: http://arduino.cc/forum/index.php/topic,107591.0.html
If you have any diagrams of what you have that would help us understand.
Most of us who have ever built automated equipment have struggled with this kind of thing from time to time, and learned to take careful precautions. Otherwise some of the fun can turn to frustration.