This is usually a symptom of a font problem: Your files are using subset embedded fonts that are not following the naming convention established by Acrobat. This means that when the fonts are combined, some characters will get replaced by others, and other characters may be missing. As far as I know, with just Acrobat Standard, it's impossible to fix this issue, you need the preflight tools from Acrobat Pro for that.
How did you create the files?
Karl Heinz Kremer
PDF Acrobatics Without a Net
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