Colors display differently between two files

I've created two billboard files; one is 96" x 48" and the other is 48" x 48". Both files were created one right after the other with identical graphics. There is one rgb jpeg of the sky, and a vector graphic with a Pantone fill. The vector graphic has a drop shadow and is in a layer above the jpeg.
The 96" panel appears fine.
The jpeg in the 48" panel becomes noticeable darker when I apply the drop shadow to the vector graphic. Before the drop shadow is applied, the jpeg is quite saturated in appearance. Once the drop shadow is applied the entire jpeg becomes noticeably darker.
If I export both files as jpegs, from InDesign, the results are completely different. All of my color settings are identical for both files.
If I turn on Proof Colors in the view menu, both files darken to the appearance of the 48" file.
Why does the 48" file darken when I apply a drop shadow, and not the 96" file?
ID CS4 6.0.4, iMac G5, OS 10.5.8

Transparency Blend space is cmyk; Flattening was low but I've changed it to medium. The Pantone fill is a spot color. Final output will be jpegs exported from ID and sent to a sign shop.
Working spaces are Adobe RGB (1998) and US Sheetfed Coated V2. The image in the files is a jpeg with an embedded Adobe RGB (1998) profile.
Right or wrong, both files have identical settings so why was one displaying so differently from the other?
I recreated the offending file from scratch and it is now behaving as I intended it to. I have a lot of these files on the go and I'm wondering if one of the them might have been created in CS3 and the other in CS4. Perhaps there is an issue with a legacy file being upgraded to CS4 as opposed to being created in CS4.
Thanks for your time.

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