Maybe I misunderstood this:
"was the missing in font, wrong character used 'uniformly' throughout the document?"
The only character that prompts this problem is a space, and then only a space used in particular circumstances, among them (but not necessarily uniquely) the font tag pair. But what appears in the ereader is not a space - rather it appears as a question mark or (depending on the ereader) whatever character is used to indicate a character that is not understood by the ereader.
So yes, it is a space prompting this problem, but what one sees in the end result is not a space. And not all spaces create this problem.
If it sounds quirky, it because it is.
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