All of the SCXI modules can be used in the same chassis with no problems. There's not enough information here to give you any specific advice, but check you can: 1) Put your DAQ card (the one controlling the chassis) in differential mode. 2) Check your signal connections for proper referencing of you signal sources. 3) Try connecting the channel before the 'inaccurate' signal to ground and include it in the scan list. If it cleans up, then the output impedance of that source is is probably too high; slow down the channel clock rate.
I use SCXI 1001 chassis with 2 SCXI 1101 and 2 SCXI 1120 with SCXI 1200 controlling the chassis. I read all channels without any problem. Just as tnewton stated, the DAQ card controlling the chassis may hold the clue to solving the problem you are experiencing.