Mag question

[Jerrytex]

I started my Rotax 912 up today and it seems to run great. The engine had 17 hours on it when the plane crashed so it is essentially a new engine and runs like a top. However, I did run into something that I have a question on. When I checked the mags, one side seemed to behave as expected, i.e. rpm dropped about 100 rpm and it was smooth. Turned that mag back on and it returned to normal. I then turned off the second mag and the engine started to loose alot of rpm and started to run real rough as if it was about to die. I turned the mag back on and it smoothed right out and started running strong again. I checked all the connectors and everything looks good. It is apparent though that the white plastic connectors that go to the ignition (four wires in each plug) can be interchanged. The guy that disassembled the plane before I bought it marked everything upon taking it apart so I put it back exactly as it was before so I am pretty confident that I have it connected right. I am familar with the Rotax mag check as I had a 582 in my PPC and did the check before every flight. This was suprising to me and there is obviousy something wrong. Any ideas? Thanks.

[Av8r3400]

I would check the plugs, wires and especially the boots that connect to the plugs on the ignition side that is showing problems.