Curiouser and curiouser! Have you removed the GFCI receptacles shown in your picture to see how they are wired? It appears as though both receptacles are GFCI's from what I can see. Normally, if they were on the same circuit, a single GFCI would be used with a conventional receptacle daisy-chained off of it's "load" side so that both receptacles would be protected by the one GFCI circuit. Also, are the circuit breakers that feed these two circuits conventional breakers or by any chance is that GFCI breaker that is shown in the upper right corner of your panel involved?
I don't see where your blue plastic box with the GFCI receptacles is being fed from unless it is the unprotected (!) black, white and possibly a green conductor that appears to be wrapped around the flex and disappears back toward the metal box on the left. If these are the feeders, they should be protected (changed to a piece of romex, perhaps). Is that black wire pinched between the plastic box and the foil on the ceiling? Also, if that is a green ground wire feeding the plastic box, where does it tie back to ground if there are no ground wires leaving your panel?
I don't see any pictures in this thread. I noticed before where you mentioned pictures and came to the conclusion that either I was blind or you had some inside information on things.
Anyway, pictures would definitely help. At least a person would have a visual image of what is being discussed.
So I got to digging through some pics I had saved for another guy who was having trouble with 3 and 4-way wiring. I thought maybe they may be of use to help explain what your dealing with or just maybe something would click for the OP.
There are several ways to wire up a 3-way circuit, and it would be very difficult to cover them all.
I will touch on one of the most common and easy to follow methods.
Step One
Bring the power supply in to one of the switch boxes (one hot, and one neutral), on a #14/2-wire cable.
Step Two
Then, run a #14/3-wire to the other switch location.
Step Three
From the second switch, run a #14/2-wire up to the light box.
Step Four
In the first box, splice the neutral (white) wire from the power supply to the white wire in the 3-wire cable going to the other switch.
Step Five
Attach the hot (black) wire to the common screw on the 3-way switch.
Step Six
The red and the black conductor from the #14/3 cable will be called the “travelers”, and will hook up to the two remaining screws on the switch.
Step Seven
At the other switch location, you will hook the white wire from the #14/3 to the white wire going up to the light.
Step Eight
The “travelers” (black and red) from the #14/3 will connect to the same screws as on the other 3-way switch, and the black wire going to the light will tie on to the “common” screw.
This method is probably the most common that I have run across, and all the wires meet at a junction box.
The most common source of confusion and problems is that so many electricians will cheat and use a neutral or ground wire from a single 14-2, instead of pulling a new run.
You also have to be careful because, as you can see: the wires don't always connect to a wire of the same color.