I will try to clarify, if someone can venture a guess I would be grateful.

Box 1 - SIngle Pole Switch - Controls 3 lights.
Black (HOT) Red connected to switch. That red wire is joined with a second black wire. There is also a capped red in the box. 4 wires total.

Box 2 - 3 way switch - Controls 2 of the lights when switch in box 1 in on. Black connected to common. Two reds at the travelers. All 3 hot when box one switch is on, all dead when box one switch is off.

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Are thw two reds in box one travelers and the two blacks would be the common? (To connect to 3 way switch I would pigtail blacks to common and each red goes to the travelers?

You didn't mention any neutrals. How are they connected? And I think you'll have to tell us about how the lights themselves are wired up.

You'll certainly need to get rid of that single pole switch. Is that a new addition/replacement?

I cant get at the 3 lights junction boxes and there are no white wires in either box.

The second black in the box actually controls one of the 3 lights. With that second black capped off.... 2 of the lights act as they should with 2 3 way switches.

I guess I am having a hard time describing what I have going here. I tried a few configurations at the first switch box but I cant get the switches to control all 3 switches.

Let me add this is off a garage subpanel that has 2- 20A breakers tied together so I assume its sharing a neural.

The extra black wire in box 1 controls one of three lights (single pole, one of the red travelers are capped).

Is it possible to cap one of the travelers in box 2 (3way switch, 3 wires in box) and installing a single pole there?

Is there a hazard keeping it as it is now. ??

ie: One box with single pole controling all 3 lights. Second box with 3 way only controling 2 of the lights when power is on at switch one.... no power to switch when switch one is off.

Again about the hazard, is this a fire/shock hazard or one of those things that it works or it doesnt?

Let me ask anotherway, I probably arent making sense.

If there are neutrals in either box. THen the neutral is at the fixture right? The wiring in the boxes are switch legs.

SoI can control 2 of the 3 lights with 2 3-way switches but that leaves a lone black wire in box one which sends power to the third light.

I could hook that black to the common in box 1. So from box 1 I should be able to control all 3 lights but box 2 I would only be able to control the two.

Have I made this even more a mystery?

I meant to say no neutrals in either box, all wiring at switches are switch legs.

If the entire subpanel are sharing neutrals (2-20A breakers tied together) then it wouldnt matter where I would put that extra black switch leg for the third light. Even if there was a second switch in box controling a totally different light... I could pig tail it to that switch and since the neutrals are shared everything would be proper?

Your probably thinking im nuts, or ready to tell me to call an electrician.

I tried to draw a diagram in order to get some help, please take a look at link below.

Here is a link that might be useful:

I'm still confused. Might be best to call somebody and sort that all out. The "two reds" in your diagram doesn't make sense. If switch D is a switch-leg, I'd expect some 14-3 wire coming to it. A black/white/red. Yes, the white would be used as one of the travelers but two reds? Is that red tape? Red sharpie?

no there are no whites in these boxes and the travelers are both red wires.

If I leave switch D as wired (black=common red on each traveler) and then wire switch C with a 3way and connect black (LINE) to common and both reds to traveler. Then the two switches act as they should controling lights A and B.

That leaves the extra black wire in box 1 for the third (C) light. I am unclear on where to pigtail this wire.

I guess my descriptions suck. But it comes down to this I think:

The extra black is a switchleg for the 3rd light. I think they used the hot (line) originally intended for this light to give power to a new fluorescent light.

Im thinking the fix is to pigtail that extra black switchleg to the switch for the fluorescent light and then that switch will control both the fluorescent and the third light.

This is on subpanel with 2 -20 amp breakers tied. I think neutrals are shared then.

If the neutral at the light is on a different leg than the hot (line) on the switch... is that improper/dangerous?

Using a double pole break may indicate a shared neutral or it may not. You'll have to check in the box. I've seen double poles used with multi-gang switch boxes controlling independent circuits. You don't want to turn off one breaker and leave part of that box still hot. By using a double-pole breaker, you ensure that both circuits inside that multi-gang box are dead.

And for your description, I didn't pick up on the fact that light #3 seemed to be added later. So you now are wanting to control light 3 with the single-pole for the fluorescent and not the 3-way for the other lights?

THe fluorescent was added later, I think they used the line feeding the 3rd light for it. Then tied the switch leg for the 3rd light into the other.

What happens if I hook up the switch leg for the 3rd light to the fluorescent switch and it turns out the hot and the neutral are on different legs of the subpanel?

Heres a crude diagram:
http://tinyurl.com/k29b79a