PDF file looks fine but prints fuzzy

Hi, I am making music books for a publishing company and we are having an issue with some PDF's. To let you know what we are dealing with I will provide you with some critical info.
I recieve 600 DPI scans as PDF's of books with music in them from our production crew. I take these files and I have to edit the layout of music on the last page so that there is room for our barcode. I insert the barcode and resave the file as a flattened 600 DPI PDF again. Then in Acrobat, I replace the old page, with the new page containing the barcode. The new page looks fine on screen, but when printed out it looks very fuzzy.
I have noticed that this also happens to our barcodes when importing pictures into Quark. I have tried saving the barcodes out as TIFF's and as GIF's (they are high contrast black and white, so GIF's have good quality and very low file size)at 600 DPI. Then we export PDF's from Quark and get the same problem with the fuzzyness.
Does photoshop have some settings for PDF's that will fix this? I am not even sure why it is doing this in the first place. I appologize for the long explanation but would rather have it be clear the first time. Any help you guys can give me would be great!
-JP

Okay thanks for the input, but when i try to import with images, instead of pages, it says there was a program error and it fails to import. Unfortunately I have to do these in photosjop first, because like I said in the first message, i have to edit the music on the page so that the barcode will fit.
The page is FULL of music, and we cannot simply shrink because that makes it harder for people to read the smaller notes. So I have to move the measures closer together, and sometimes I have to cut out extra space in the measures. If I were to do this in quark I would need to set up several different image boxes and then make sure they would line up properly. It is not very time effecient because I do dozens of these each day.
I have been playing around with the downsampling options and I am getting better results with that. I will post any progress I happen to find.

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