I've made quite a few images in Illustrator that have gone into LaTeX documents before with no problem, but now I'm having an issue with a graphic that has some gradients in it.
I've tried exporting it from Illustrator as a pdf with almost every combination of settings I can think of and they all seem to have issues. To demonstrate, here are some screen shots of just one small part of the graphic:
In Illustrator (what it should look like):

Exported as pdf/x-3 and viewed in Preview (weird boxes showing up, looks the same in LaTeX):

Exported as pdf/x-4, in Preview (looks good!):

That very same pdf/x-4, in my LaTeX document (probably worst of all of them!):

So, there is obviously some strange stuff going on with those boxes showing up and gradients disappearing and whatever else is happening in the last example, but I can't figure out what the issue is.
I know it sounds like I'm complainting about an Illustrator issue, but there are plenty of versions I export which look totally fine in Preview and other programs, but when I run them through LaTeX, they look all screwed up.
Any ideas on this? The graphic is in RGB so I am guessing it may have something to do with going to CMYK, but I don't know how to do that while still having it look good. BTW I am on a Mac, using TeXShop.