Apologies if this has already been answered, but given what I've read so far, the most obvious thing to check (for me) is that both analog input cards have been configured the same in Logix 5000 (or Studio 5000). For example, one card could be configured to read 0V as 0 and 10V as 10000, while the other might be configured to read 0V as 0 and 10V as 12000. This would give you an error like this.
Before I got to that stage, I would (as others have suggested) put a high-precision voltmeter on both analog inputs and compare the readings. There is no use any of us, the OP included, taking shots in the dark when some simple tests could provide a lot more useful information.
Also, as I asked previously - has this only started happening recently, or has this problem always existed, since the transmitter was first installed? That answer will also narrow the field of possibilities a lot more.
Before I got to that stage, I would (as others have suggested) put a high-precision voltmeter on both analog inputs and compare the readings. There is no use any of us, the OP included, taking shots in the dark when some simple tests could provide a lot more useful information.
Also, as I asked previously - has this only started happening recently, or has this problem always existed, since the transmitter was first installed? That answer will also narrow the field of possibilities a lot more.