Colors get messed up when exporting to adobe pdf

I am working on a book cover that is mostly black. I have an image that has a black background that i have placed on the cover, and then i created a box and filled it with black for the rest of the cover. When i convert to pdf there is a noticible difference between the black of the picture (darker) and the black of the filled in box (lighter, almost looks grey). If i export to a jpeg it is fine, the colors blend seamlessly. What is going on? How do i fix it?

There is a lot that goes on with Blacks and exporting. First off, your image is probably photographic, or some sort of continuous tone raster image. If it is, and you are dealing with a naturally captured background, the black will have some variation from area to area, and it will have either R,G, and B components, or it will be a blend of the four CMYK channels. There's a good chance, from your description, that the black background you are placing it against is a frame filled with the [Black] color swatch, which is just 100% K ink without other components.
Adding other inks with 100% K results in a darker black, possibly with a cast toward another color, but still a color you would call black. Themore additional inks you add, the darker that black becomes, and 100% k, when printed, looks like gray in comparison. You may also have your preferences set to deceive you. In the Appearance of Black section, make sure that you have Display All Blacks Accurately set to show you the difference on screen.
When you export, colors can be preserved or converted to a destination profile. If you are converting RGB to CMYK, you will get a 4-color "rich black" equivalent. If you are converting to a different CMYK space than you have set for your working space, and you don't "preserve numbers," your 100% k will also convert to some four-color mix, but one that is lighter to simulate the single component black. If you convert to RGB, your blacks will convert to three-color RGB mixes.
What this means is that unless your image has a "dead flat" color (i.e. an artificial background that you've added in compositing an image) and you fill your drawn background in ID withthe same color mix (and are using the same color space as the image for your working space), there is virtually no chance of getting a seamless transition from image to ID background.

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