Images will break up into pieces during the "flattening" of transparency in the PDF creation process. The size of the pieces are dependant on the Raster/Vector slider in the transparency/flattener settings. These days, there are many sources of transparency. Here is a cut and paste:
In Adobe CS2 applications, a graphic object is a source of transparency if any of the following applies:
- It has an opacity of less than 100 percent or an opacity mask (Illustrator).
- It has any blending mode other than Normal.
- It has a drop shadow or feather.
- It has a inner glow or outer glow effect (Illustrator).
- Its fill or stroke has a style, brush, pattern or filter effect that has any of the previous properties.
- It is a placed Photoshop file (native, PDF or TIFF) with a transparent background.
- It is a placed Illustrator file (native or PDF) that contains one or more objects with any of the previous properties.
It doesn't really matter what appz are involved, if you are making a 1.3 (acrobat 4) PDF it will be flattened. If you make a 1.4 PDF or above, the PDF will still contain transparency until the RIP gets it's hands on it. Some RIPs can not handle PDFs above 1.3.