@Doitsu, thank you. I have gone looking for ligatures and found that one Burmese computer fonts specialist has encountered similar problems with the Burmese fonts and tried to develope his own fonts with ligatures. He has identified 2200+ glyphs which works in CS3/4 and Indesign but they are not supported by Indesign CS5.5. I will have to explore more on this ligatures. Devanagiri also use some ligatures.
I think mainly it is the ADE which is not supporting the font to incorporate in epub.
For your info and testing I am enclosing a short epub as described in my previous screenshot(3). I will also include the Word version.