First one other thing,
I/O map picture has *5E04xx FPUSEL and *5E08xx FP[V/Y]POL.
Maybe latter is polarity something.
Since clock is clearly working, no overly short pulses, keep it.
Trigger is different, I don't really understand how this machine operates behind the scenes.
Getting Started Manual section 5 is for Timing Analyzer.
There page 5-6 has a picture of 2 defined labels, page 5-8 has defined 1 edge.
After that it does Run and after that it shows a Timing Waveforms display and all waveforms are the same.
There label is named RAS but display is RAS 00 for all rows.
After that it changes the 2nd label to CAS and display is CAS 00, can't say what that 00 is.
So you should be able to do the same and change all rows to their individual pins that you have assigned earlier.
After that your picture should be so that all labels are different, triggered to 1st label and rest are what they are.
If you have not assigned any pins to other labels they all should be the same, up or down.
Your picture should also be so that triggered situation is center of the screen.
If you now want different waveforms you do new Run, or scroll around to see what other things have happened.
One difference between manual pictures and your earlier waveform pictures.
Manual picture has 'to trig' fields on the upper section, so maybe your trigger has never actually been there.
Above Then Find Edge field is Present For fields.
There must be something, > 30ns is fine.
It means that triggering level must stay longer than 30ns before it is accepted as a trigger.
External trigger input is for Armed by field of Timing Trace window and BNC Input selection there.
Don't know how it operates, maybe it's for general start of data collection since its other selection is Run.
I also remember from somewhere that some analyzers are tricky, maybe this is one of them.