So I thought Id ask here.  Any help on this is appreciated guys.

I have a very simple scene where a glowing ball of light travels into the scene, over the camera (which is tracking it) and into the distance. 

My node set up (as pictured below) is two render layers. 
The base layer contains the scene and the object within the glow, in this case a simple black square, and a green plain object to serve as the ground. The base layer Include settings (pictured) has all options checked except zmask, neg and All Z. Visible layers 1 and 6 are selected. Scene Layers included in the Render is only the 1st.
The glow layer contains just about everything else, being the glow object itself (a copy of the black square given a different material), all lights (two points and a sun), 6 area lights parented to the glow object. The glow layer settings (not pictured) Include are zmask, solid, halo, ztransp, edge, strand. The zmask layers selected are 1 and 6. The Visible Layer selected are layers 1 and 6. Scene layers included in the render is just layer 6.

My problem concerns the actual compositing of the two layers together. When the actual compositing gets done my sky darkens preceptively. I can only think Ive done something wrong in my node set up (which works perfect for the glow effect i want) or that I need to disable sky in the base render layer, create a third RL and enable ONLY sky for that layer and then mix it in to the node set up (or would I use an Alpha over for that?) 

Hi CDI,
With amount of bugs being introduced every day by so much being added, I would guess that this is some type of bug. There are issues with nodes...rendering...texture/material assignment in World UI...just to name a few.  In one bug fix, the atmosphere is "disabled"  "when the sun lamp direction is below the horizon and needs to be recoded". This sound like this may or may not be your issue. I have not tried 2.5 in weeks.

Can read here...
http://lists.blender.org/pipermail/bf-blender-cvs/

I've given up on using 2.5 until it's out of Alpha release and may even wait till 2.6 as some have said they would do also. Mainly because of B_mesh being on hold till who knows when.
If you have personal contact with a developer that is working on this part of blender, I would contact that person, then file a bug report. If your a noob like me and do not have any personal contact with developers, then you may have to wait it out like I am and forget about sending a bug report. There dumping bug reports from new users. I've had it happen to me. I have no idea why? I do know that they are very touchy when asking why!

I truly wish that I had a solid answer for you...I hate it when I need questions answered and can not get any...anywhere.
Have you tried this set up in 2.49b to see if you get the same results? If it's the same, then it may be a carry over bug from 2.49 to 2.50.
Please post back if you get an answer, I am interested to know if it was the atmosphere getting turned off in that "bug fix" that's causing this.

 3d

Actually I think that might be it. 
One sec and let me check. 

Solved!!! 

You my friend, rock!

As far as devs go yeah I dont know any of them. Even if I did I doubt Id bother them. 
In my experience filing a bug report, similar to posting this same question at blenderartists (the so called premiere source for help with blender), usually gets ignored, blamed on someone else or writtin off as currently un fixable. shrug

As usual though renderosity forums come through for me. 

I love you guys. 

Glad to be of some help...I was looking at the commits for the past 24 hours that day and remembered seeing the commit on that so called bug fix and kind of chuckled at the fix. When I saw your post, I remembered that the atmosphere was disabled...which should result in some sort of change in the render.

2 years ago, all the developers agreed that no new things were to be added to 2.5 until 2.49 was ported over to 2.5. beta version. This did not happen. Thus the reason were still in a alpha stage, and just about every part of blender is broken in some way, shape, or form.

I saw your post at blender artist.org...I must thank you for the laugh I had when reading your reason for editing your post...how true. I have not been there in about 6 weeks now...the same reason, lack of help. Here, I'm having a short conversation with myself:
http://blenderartists.org/forum/showthread.php?t=181309
As you can see...it's a valid question...at least I thought it was. By the way, this issue is caused by the "Smooth View" being broken...set the smooth view setting from it's default setting of 250 to 0.

If your post count is low or have not been there more that 3 years...It's like you do not exist.
To have the Blender Foundation direct users to that site for support is shortsightedness at best.
My partners here in the office are now having second thoughts on my Idea to get blender into the pipeline, mainly because of present support issues. I'm beginning to see the wisdom on this matter. Ton Roosendaal needs to address this issue...now. I see other company's raising
this issue also.

Again, happy to be of some help...later.