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Which versions of the various components are you using (CUPS, pdftpdf and Ghostscript) ?

Have you checked the intermediate file produced from pdftopdf to see what that PDF file looks like ?

Have you examined the CUPS raster produced from gstoraster to see if it is correct ?

Exactly how big a difference are we discussing ? A pixel, an inch ? Bear in mind that this is apparently a 203 dpi device, so a pixel is quite a lot.

Given that there are 3 stages in the pipeline the first thing you should do is attempt to isolate which step is causing your problem. First capture the output at every stage; the PDF resulting from pdftopdf, then the CUPS raster file resulting from gstoraster. You can examine each of these individually to see if they show your problem. If they do not then the problem must arise from the final step 'rastertoezpl' and you'll need someone who knows that code. Otherwise you'll be able to decide whether the problem is the pdftopdf step, or the gstoraster step. In any event you can then ask for specific help.

Its most unlikely that the content of the PPD file has any impact here (other than specifying the final filter required to drive the printer). Of course, without seeing the original file, its hard to tell, possibly the barcode is a TrueType font.....

[edit]

Well I still can't see a Ghostscript command line in your question. I'm not able to run CUPS and I can't build RasterView either since it requires a bunch of dependencies I simply don't have.

However, I can run it to TIFF. The result is the same as your photo when the resolution is low enough.

Your problem is the one described in comments 17 and 18 in the bug thread I posted in my comment below. The PostScript (and PDF) imaging model says that when any part of a pixel is touched, that whole pixel is rendered to the output.

Your PDF draws the barcodes as a series of (vector) rectanlges, using co-ordinates and sizes which are not precisely aligned on the underlying pixels of the device.

If you use Adobe Acrobat and 'save as' TIFF you will see exactly the same problem there (you need to set the resolution of the output to 203 dpi using the 'Settings' button on the 'save as' dialog).

There is a long discussion on the bug thread about this, there are a number of possible solutions;

1. Write the PostScript (or PDF) so that the co-ordinates are precisely clamped to the device grid. This may be difficult to do, especially if you run the file through pdf2pdf.
2. Draw the bars by first drawing a big rectangle, then draw the spaces between bars as white.that might make the bars 'skinny' but they won't merge. If the printer is thermal then the thermal spread will reduce the effect.
3. Generate the barcode as an image instead of vectors. Images don't follow the 'any part of pixel rule', they use 'centre of pixel' instead, which may give (at least slightly) better results.
4. Use a barcode font. Fonts also use a different method for drawing, because if you reduce the font size it quickly turns into a series of black blobs if you use any part of pixel.

Basically, you are trying to draw shapes to a tolerance which simply isn't possible on a low-resolution device like this, when using PostScript/PDF.