As many of you already know, Pantone colors were once named with "CVC" and "CVU" after their numbers. These were to indicate Computer Video Coated and Computer Video Uncoated. But in the year 2000, Pantone switched to a universal naming scheme, using only C for coated, M for matte, or U for uncoated. But since the naming itself wasn't enough, Pantone also changed the actual color breakdowns, or CMYK representations of those colors. A new Spot to Process Guide was published as well.
Illustrator 10 was the first version of Illustrator to use these newer libraries (according to Adobe's licensing agreement with Pantone, Adobe is required to ship their products with the latest available libraries).
This opened the doors for a potential problem: If you opened an older Illustrator file that used an older Pantone CVC number, the CMYK equivalent of that color might not match the newer CMYK equivalents found in the newer Pantone C libraries that ship with newer versions of Illustrator.
In reality, if you are specifying a Pantone color, and are printing it as a spot color plate, the underlying CMYK values really don't mean much (except for proofing). But on press, everything will be fine, as those CMYK values are never used.
However, many designers use Pantone colors -- and those colors are many times converted to process later in the workflow -- either by another designer or by the printer. This can cause color shifts where the older and newer colors appear.
For this reason, the release of both Illustrator 10 and Illustrator CS also shipped with both the newer C libraries as well as the older CVC libraries, so that users could load and use the older CVC colors and migrate to the newer colors as they were ready to do so. Basically, Illustrator will allow you to import older colors in an unchanged state, and you can choose to manually move to the new colors -- thereby retaining the integrity of the older files.
However, InDesign chose to take a different route to address this problem.
As a page layout application, InDesign is used to aggregate content from other sources and applications. When you place content into InDesign -- for example, an EPS, a PDF, or an Illustrator file -- InDesign will look for any spot colors in that file and add those colors to its own Swatches palette. Now, if you already have a newer Pantone C color that exists in your file (say for example, Pantone 485 C), then if you place an older Illustrator file with a Pantone 485 CVC swatch, the result will be TWO plates in your InDesign file -- one named Pantone 485 C and one named Pantone 485 CVC. Because of the difference in the name, these colors will separate on two separate plates.
To prevent this from happening though, InDesign has code that can recognize the names of Pantone colors. When InDesign sees a Pantone CVC number, it imports it and merges it into the same swatch as the C number -- meaning if you place a file with Pantone 485 CVC into InDesign, that color is automatically merged with the newer Pantone C number -- and the result is a single plate. Which is nice. But there's one problem -- in this process, InDesign uses the newer Pantone C CMYK equivalents of the color. In fact, even if you import a CVC color into InDesign, and you don't even HAVE an exisiting C color in your file, InDesign will recognize the CVC number and automatically convert the CMYK equivalents to match the newer book color (the C values). This means there is no way in InDesign to preserve the older values, if you had wanted to. That means if you convert that spot color to process in InDesign, the color values will change -- and there's nothing at all that you can do about it.
You can argue whether InDesign's behavior is correct, or whether Illustrator behavior is correct, but the end result is that Illustrator and InDesign are not consistent, and you'll see different results depending on which app you print these files from. I should point out that Acrobat will mimic Illustrator's behavior here -- so printing from AI and Acrobat will give you the same result -- but printing from InDesign will result in something different.