Question about FIR filter outputs

Why are you worried about 3 missing outputs? They're probably gone forever because of latency. Also, are you using the avalon data out valid signal as your "data valid" signal or just sampling it according to your data in side, if you are that's a no no? :) I bet if you run 10000 inputs you'll get 9997. I tend to look at the streaming data anyway in signaltap. The first n samples out of an n stage FIR will be invalid carp data anyway. Why not run 10000 samples through and grab the most recent 5000? or at least give time for your fir n data stages to fill up. Put an impulse through it and see if that helps to determine the problem.