Art is mysteriously disappearing or moving to undesirable location when exporting to PDF

I'm on ID CS5 on an iMac, OS 10.6.4
I'm working on a book cover series. I started it last fall in ID CS3, front front covers and spines (for marketing files). Now, with the InDesign multiple page size feature, I thought this would be the perfect project to try it for the first time. I started a new document with a Master page for the back cover, another for the front cover, and 3 versions of spines with slightly different widths. Each spread consists of 3 pages.
2 weird things are happening.
One. When I export a PDF (either press res or a low res) the logo on the back cover disappears from the PDF on pages 1 and 2, but is present on pages 3, 4, 5. (The PDF pages represent the spreads for a 5-volume set). It is on the master page and has not been altered or released on any of the pages, yet views differently.
After trying different things, I did finally get it to appear, but it appears half cut off on the bottom of the front cover on pages 1 and 2. Not at all the place I need it to be.
So strange.
The second thing is that I was making some minute adjustments to the placement of a box on front cover master, and all of a sudden, it shows up centered on the whole spread on the 2nd, 3rd, 4th, 5th layout spreads. I mean it is far off from the small move I made on the master.
The art is so jumpy you'd think it was on speed.
Help? Advice?
TIA,
Anne

Well, I fixed it. Not sure what did the trick, but since it has to go to the printer in the a.m., I'm just happy it works now.
I recreated the graphic (logo) in Illustrator and imported it as EPS. Previously I just copied and pasted between documents because the logo is just outlines/shapes. Then I placed it on the back cover master and exported as highest version of PDF. And everything is where it's supposed to be.
But that other wacko jumpy behavior persists.

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My InDesign files are too big to upload anywhere, but these two screen shots show an example of this problem.
This is how the spread looks in InDesign (link and effect info for right image shown):
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