To determine what happened with your second coat more information is needed.
How did your first coat go? Did that have lumps or finish "pulling away" from areas that you applied it? Did your first coat cure fully? Remember Epoxies Cure, they do not Dry, its a chemical reaction, nothing evaporates from the mixture, unless you "thinned" the mixture by adding something like DNA or Acetone, then either of those two will "off gas" while the rest of the mixture cures, some of it can remain within the cured mixture, but that is a whole other conversation on whether or not that is a good thing.
Did you do anything to the rod between applying the coats of finish, like wipe the rod down? Touch any of the wraps with your fingers? The natural oils in our skin can cause issues, also if you "cleaned" the rod between applying finish, like with a "tack free" cloth, they have chemicals in them that cause dust particles to stick to the cloth, but it will leave a film on the first coat.
What speed is your rod dryer running at? For curing finish no higher than 18rpm is recommend, the ones that turn at 6 to 9rpm are best. Goes back to that first coat question, did that go on as applied and cured okay? If your speed was too high, your finish will lump up, and if your rod is not level, that will also cause the same problem, when rod is not level, finish will leach towards the low end.
Contamination, between coats, what did you clean the brush with? The Rod Dancer, U-40, or Flex Coat epoxy brush cleaners will clean a brush properly, as a final clean after using these products (and they can be interchanged) you can clean a brush with 90% Iso Alcohol, although it is not necessary.
How much finish did you apply? If you over applied your finish, putting way to much on, it will "lump" up, or take on the the appearance of a "football" look to the wrap (American football). Just look around at others finish work, you can see the ones that look nice, level, flat. The ones with a large hump in middle, they applied way to much finish.
Did you pour the finish out onto Aluminum foil before applying it? One side of Aluminum foil has a "release agent" on it, the shinny side, its there so the rolled up sheet does not stick to its self, should be obvious as to which side to pour finish onto.
Thread Master finish? Lite or Regular? Both have very different working times, by working time I mean the amount of time you can apply the finish before it sets up to the point where it will not flow and self level. Regular Thread Master has a short working time and it is not as viscous as the Lite Thread Master. This could also be your issue, finish setting up before you got the whole rod coated. I use both of these products all the time and I have for years, the Lite formula for all my builds due to the longer working time, the Regular for when I just need to repair a broken guide or two.
If you can, provide more detailed info to my questions. Also take a look at this link below, its how I apply my finish.
Your best bet may be to remove the finish and thread and start over, tread lightly doing this, like some of the others that have stated above, you can remove the paint on certain blanks if you are not careful. Also tread very lightly with heat when you try to soften the epoxy for removal, very little heat will be needed since the epoxy is still not fully cured at this point, it usually takes several days for it to reach full cure, by that I mean you may be able to "dent" the finish with a finger nail, even after it does not feet tacky after an overnight of sitting in a drying rack. Too much heat will also damage the resins that bind the glass cloth together.
Good luck
Oh, the plug in air freshener, not the problem. Also, Google "Fish Eyes in Rod Building Thread Finish", you find answers to what causes that.
http://www.rodbuilding.org/library/betterepoxy.pdf