I have a similar experience with vertical border lines, in Acrobat parts of the border seem to be one pixel wider (or smaller) than others. Since it is always a pixel, no matter the zoom factor, and it is not visible in print, I ignored it...
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I'm using FOP 0.95 to build PDF files from XML files.
I found a strange thing on rows borders : when I have more than 2 columns in a table, rows borders are strange. In fact, only the first and the last columns borders are well drawn, all other columns ar not. On the "fo:table"
element, the "border-collapse" attribute is valued to "collapse". Here is an example (only the third table is well drawn and there are the problem on the lines between the lines "ligne1" and "ligne2" ans so between the lines "ligne3" and "ligne4") :