Is there a maximum encoder pulse rate the system can handle?

[The Lucas]

Are you encoding in 1x 2x or 4x mode?
Max counts per rev for 102v is 2048 (I guess you are prob using 2x for 4096).
It is doubtful you are overloading the FPGA of the rRIO with your drive train moving slowly. Calculations I have seen on CD have the rRIO capable of about 5 million counts per sec.
http://www.chiefdelphi.com/forums/sh...5&postcount=12
Check your B channel to see if it is operating correctly (since it gives you direction only, unless you are in 4x mode). You can do this with a moderately advanced multi meter that has a Hz function. Or you can simply swap the A&B channels at the rRIO and see if the same behavior happens in the negative direction. There is an index (X) channel on these encoders, so that might be in the mix(A or B), causing interesting results.