How are you defining your crop area?
I've defined the crop area both ways, but I usually just draw a box and say
Since it sounds like you are using CS3 or earlier from your description, the next move is File>Export to choose JPEG. You will be given a chance to select the ppi in the second Save dialog.
Ok, that works. What if I want to save my crop area as a pdf?
just jumping in because you must realize that CS4 doesn't have the croparea anymore...
I'm having somehow the same kind of difficulties. Try to use layermasking and save a copy as .eps
in this way you will get a bounding box cropped eps. Saving as PDF keeps me getting some extra space left and under the boundingbox (seems like it has something to do with text though)
This is my way (for this moment) to get different sections out of a hughe citymap.
With the eps you can get your pdf and or the JPG by placing it into indesign or photoshop..