Been trying to fly the FA18, but no joy. First, only one after burner fires (Left engine), and I can’t get the flaps to retract. Is this a known problem, or am I falling off the turnip truck.
Turnip truck, sorry 
Check your mapping/binding.
How are you activating the ab?
lots of helpful posts, search:
fa-18-super-hornet
I flew it much earlier and everything worked. I have set the Toggle Afterburner to button 4 on my CH Fighterstick, but only the left afterburner fires. I even tried setting all the after burner option to button 4, still only the left burner goes off.
Check your assistant settings, if there‘s anything that might interfer. Not sure what it could be but I actually don‘t know any sensible reason beside that.
The right engine is running, the one without ab, correct?
Have you checked that post (and look for other ones related to the F18 in the same forum category) ?:
Assign a keyboard key and try that. does it work?
You could also try toggle ab1 & toggle ab2 to the same button. Does that work?
A shut down engine would certainly inhibit any afterburner 
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I tried putting AB1 and AB2 on the same button, but no joy. I tried looking around the cockpit and discovered that there are 2 throttles. I appears the if I move both forward then both afterburners fire. Note that I have the afterburner set in the throttle, so full forward fires the burners. Do I need to configure for 2 throttles?
Thanks for the help
I fixed it. I had to config the other throttle Throttle 2 Axis. Works fine now/
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