I'm referring to Adobe Acrobat's boxes. These can be found in Adobe Acrobat Pro by opening the "Set Page Boxes" window. There is a crop box and a trim box which mean two completely different things in Acrobat. In Acrobat Pro, the crop box is the entire area that is displayed in the document (including bleed, marks, or anything else in the document). The name can cause confusion since, just like you said, crop and trim should be identical. Really, Crop Box should be renamed to something else that would make more sense. Maybe "Document Size."
When it comes down to it, the trim marks should line up with the trim box in Acrobat. Unfortunately, it doesn't. It lines up with the crop box which is whatever the document size is set to. For example, an 8.5 x 11 document with 1/8 inch bleed results with an Acrobat Crop Box set to a size of 8.75 x 11.25 inches. And that 8.75 x 11.25 inches is where it places the trim marks instead of the 8.5 x 11. The only fix I've found is to open the same file in Acrobat 9 which will print the marks in the proper location without any changes to the file.