I just finished rendering out a scene in Vue 7 and it is just the way I wanted it.  When I took it into a compositer, I noticed a problem which I can't explain.

The images attached show what's happening.  The image with the clouds is what the scene is supposed to look like but instead I'm getting the second one without all the clouds.

Can anybody suggest what's going on here?
 

Thank you

 My first guess is that you might have something set in "post render options"   
under the Render menu, scroll down to "post render options", make sure all the little boxes are unchecked.

are you rendering to screen? or disc? I always render to screen so I see what's up

I'd guess you have auto exposure on in the post render settings. 

Or you've saved it as a png or similar with the Alpha plane........

It could be the alpha render as thefixer said, but it looks more like, but not entirely the post FX Vue itself is incorperating into the image. (;