I posted my issue in the Illustrator forum, but have found in my research that what is happening is the "white box effect". When I make pdf's some ai eps's have a white box behind them.
Some fixes I've found include:
Viewing the pdf in Overprint Preview and with Enable display trim, bleed boxes.
Using pdf/x export settings.
Turning off spot colors in ink manager.
Checking "Simulate Overprint" in output settings.
They said the clipping paths were missing from the files they sent me after I had inquired, did not know why, and resaved with the paths. Sorry, don't know how. I know an eps usually had a reddish icon in the folder list and this one had purple instead when it was wrong, if anyone knows what that means.
FYI, it was confusing because the "white boxes" were not all around in a big shape like you would think if a clipping path was gone. It was a smaller white box more to one side like this white box effect illustration on that link.