I have a '94 1.8l NA miata, the running lights on the back will not turn on but everything else works. (Break lights, turn signals, reverse light). The other night when I started it up though they were all on but then when I got back home I noticed they were off again. It seems to be an all or nothing sort of deal. I checked the 2 LA10 relays on the left rear part of the engine bay switching the two around to see if that would work and it did not. I also checked for loose wires in the trunk and it didn't seem to work. The interior lights and dash lights work just fine all the time.

 

http://www.madracki.com/miata/images/wiring/94sys.pdf

Bottom of page 10 seems to tie the ones that are working to the ones that are not. Check for broken wires. Pull bulbs and clean contacts.

Madracki's wiring diagram may not be completely correct. Earlier models, while fed by the same circuit had distinct separate wire to ground and hot leg from those two lights. Run the wires back from the sockets visually.

 

And check your grounds for that part of the harness for corrosion and/or a bad connection.

 

Also, if someone added a trailer harness to the car, check that. I have seen them short out the lights before. Not too common on a Miata but some folks do have them.
My best guess is that since the issue comes and goes, you have a bad ground.