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The colors don't have any impact. In fact, colors are also used to indicate page changes in the original document (if you use the post-OCR routine). The only thing that might cause a popup not to appear, is if the routine is aborted due to an error or exception.
@Leonatus, could you sent me the document that gives this issue? The log will probably not help in this case, as in this version it is still very limited. Could you also try another document?
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