APM 2.6 Fails When R/C Receiver Connected

I just received a APM V2.6. When I do not have the R/C receiver or outputs connected, it communicates with the mission planner as expected. However, if I connect any of the receiver inputs, It fails to communicate, like it got lost in the program someplace. Does anyone know what could cause this? I never saw the problem with the APM 1.

First off, is it a genuine 3DR APM2.6?
Second, have you set it up per the ArduRover Wiki instructions: http://rover.ardupilot.com/wiki/setup/
Is J1 removed?
Have you verified that the receiver channel outputs are correctly matched to the APM receiver inputs? In other words, rtn to rtn, power to power, and receiver signal out to APM signal in. If the rtn and the receiver signal out are reversed, then the APM will not work correctly.
What R/C receiver are you using?

It is a genuine 3DR APM 2.6 (came from them). J1 is removed, because at this point, I haven’t been able to find out what it is for. Right now I only have a 2 channel receiver. At some point that’s going to change. But as I said, I never saw this with the APM 1. The other thing I find is that with the APM 2.6, with the USB connected it tries to power everything (the ESC is in alarm the whole time). I cannot get a serial connection to the Arduino IDE unless I disconnect all of the APM inputs and outputs. I never saw that with the APM 1 either.

J1 connects the APM internal power bus to the APM servo output power bus.
Here is a wiki explanation of how to power the APM and the AMP servo outputs: http://rover.ardupilot.com/wiki/common-apm25-and-26-overview/#Power_Supply_Rails_Not_Connected_Requirements_JP1_Not_Installed
It is not a good idea to use the USB to power the APM servo output power bus and I recommend that you remove J1 per the wiki instructions and power the APM servo output power bus with a separate BEC.
What R/C receiver are you using that is only two channel?
The APM1.4 and the APM2.6 input and output buses are very similar so it is interesting that you are experiencing a problem. It sounds like you may not have your receiver connected to the APM receiver input correctly.

Your description of JP1 says that this APM thinks it is installed when it isn’t. That made me think to
try something else. When I remove the power lead from the cable between the receiver andthe APM,
the APM will work with the receiver connected. Something appears to be wierd in the power section.

The receiver is a Spektrum DX2. I’m planning on upgrading to an 8 or 9 channel here at some point.

I am having the same issue I have a 2.6,whenever I hook up the spectrum 6 channel receiver all fails,sometimes I connect but no data,when I remove the receiver all goes back to normal the 2.6 sends data,could be a generic 2.6? does that matter?