Frequency measurement, I can not seem to get the TI mode to give me anything other than negatively sloped line. I do want to see if i can arm the counter from a 1pps signal.
That's suspicious. If you measure the time interval between two oscillators at slightly different frequencies, the result should gradually drift through all values until it reaches an interval equal to the period of the frequency involved and then wrap back to zero. The numbers could increase or decrease depending on which oscillator is faster or slower. On a graph it will look like a sawtooth. e.g. for two 10 MHz signals, the result should go from 0 to 100 ns. If the frequency difference between the sources is too high, you won't see the sawtooth, it will just look like random numbers in the same range. If your counter can't do that, it makes me think there's something wrong with your counter which casts suspicion on all your results.
I know that earlier in this thread, KE5FX recommended frequency measurement. I've always preferred time interval because some counters work
much better in that mode. My HP 5370B and Wavecrest DTS-2077 are like that. Also, with time interval, you can be sure that you're only measuring one interval and aren't doing any averaging which will artificially improve your results. I think that's what's happening in your recent results.
Ideally, the start signal would be 1 PPS and the stop signal would be whatever the DUT (Device Under Test) provided. Configure the counter to use its internal reference. It should be able to take the reading and reset before the next pulse so deadtime shouldn't be an issue.
I'd recommend that you take another look at time interval mode. Timelab understands phase wraps and does a pretty good job of unwrapping them.
Ed