i think i have found the source text used for the "lilly white, comely queen" lyrics. I was reading through one of my mediaeval english lyric books and by chance found this. the text is anon and dated c. 1500:

the lily-white rose:
this day day dawes
this gentil day day dawes
this gentil day day dawes
and i must home gone
this gentil day dawes
this day day dawes
this gentil day dawes
and we must home gone

in a glorious garden grene
sawe i sitting a comly quene
among the floures that fresh bene
she gaderd a floure and set betwene
the lily whighte rose me thought i sawe
the lily whighte rose me thought i sawe
and ever she sang

in that garden be floures of hewe
the gelofir gent that she well knewe
the floure-de-luce she did on rewe
and said "the white rose is most trewe
this garden to rule by rightwys lawe"
and ever she sang

However, the actual lyrics for "lilly white, comely queen" are arranged somewhat differently:

lilly white, comely queen:
this gentil day in glorious garden grene
sawe i sitting a lilly white comly quene
gelofir gent that so she did love knewe
in his place a floure most trewe
[and for noel*] lilly white virgin quene

*not sure about this part, this is just my estimation; it was the only line i could not decipher as taken from the source text, any suggestions are welcome.

Taking into consideration what some of the Baebes have said regarding how Martin Phipps just took mediaeval english and latin words from various texts and put them together randomly, i think "the lily-white rose" is quite obvious as the source text for "lilly white, comely queen".

I also found this text somewhere on the web, it looks like a transcription. I do not know who is responsible for it, but it appears to be wrong:

his gentle deed in glory who was proud and grand
so i sit here a lilly white comely queen
gentle fear beheld that saw she did love anew
in his blossom a flower most true
and for knoweth lilly white virgin queen

Also since the Baebes do not have any lyrics posted on their website, I suggest anyone wanting to read them online visit: http://lyricwiki.org/Mediaeval_Baebes. It's a free resource and anyone can contribute, so if you spot an error or know of a song missing, then please add it.

Anyway, I hope this helps.

LH

P.S. Is anyone any closer to finding the source for the latin texts used in The Virgin Queen OST?