There is some unique issues with converting to Arabic such as the right to left reading style. If the format itself does not support this it's not really possible. Mobi for example does not support right to left text at all. Neither does epub 2 which is what Calibre converts things to for epub. Epub 3 however DOES support right to left text. So does AZW3 if properly implemented.
Arabic is not completely unique. Calibre chokes pretty hard on Japanese too making books with vertical text horizontal, Ruby charcaters end up in line and page flips right to left become left to right.
Other languages work fine because for example between French and English the only differences to the file formats is a handful of characters like ê and á.
I'm not sure what file formats you are going to and from but you might have better luck with other converters.
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