AFAIK, ligature handling can be defined in the font and/or handled by the word processor. Your issue might be caused by the font that you embedded or more likely ADE deficiencies. AFAIK, ADE can for example handle Devanagari letters with the correct font, if the text is encoded as Unicode.
In order to further test this please:
- name the font that you embedded
- post a short Burmese test string using Unicode letters that illustrates this problem (or a short one page epub) and a screenshot of the desired display