Arabic lam-alef ligature in vocalized texts

[Am�lie DELTOUR]

Hi,
How should the LAM-ALEF ligature be vocalized in Arabic according to Unicode?
In texts on the Internet, I find the codes in the following order for instance: "U+0644 U+0627 U+064E" (LAM-ALEF-FATHA). The logical order would rather be LAM-FATHA-ALEF.
The problem is that if the LAM-FATHA-ALEF order is used, then the LAM-ALEF ligature is not recognized in common display programs (IE, NS6 or MS Word).
If I understand the Unicode Standard well, the FATHA should be treated as a "transparent character" and should not disturb the representation of the LAM-ALEF ligature. In that case, it would only be an implementation problem of the display programs...
However, I can notice that on the Internet, in vocalized texts (Quran, Bible) the LAM-ALEF ligature is most often bad vocalized : the diacritic mark is before the ligature, or after, or in most cases is not there at all (in particular in the case of "li + alef-hamza") - which is quite annoying.
Can someone tell me more about this?
Thanks,

Am�lie

(Sorry if the issue has already been submitted to the list - I couldn't find the answer to my question in the archive)