What is the
Computers language?
Preferences: Look and Feel: Choose Language allows calibre UI to have a different language.
Lastly, what language was set in the Library Listing for that book? If that was a LTR language, that is what might affect the conversion.
AFAIK The character set does not set the direction
You might get a quick fix by adding this line to the Body style (class) in the CSS using the Editor
apologies if this is not a cure, I only read a LTR language