I have done some testing and it is indeed that the death of the jarl's housecarl breaks the oppurtunity. If you become thane of the Falkreath and you complete the Contract: Kill Helvard, regardless if you were seen doing it, the Jarl acts coldly to you, just as when first met, and the option to buy the house dissapears. This seems to be a coding error where Helvards death causes a negation of Thanehood in Falkreath. Along with that disables the ability to purchase the land. Until Bethesda patches it, the only option is to revert to a save before he was killed which unfortunately for me is 60 hours back... But spread this around so that everyone knows and Bethesda can try to fix it.
Yeah, this is particularly bad because if you're affected by the bug, as I am, you can't get the achievement for having 3 houses without making a new file. Man, that's just ridiculous. Not too many bugs really bother me because I can just sort of ignore them, but to have a DLC where you are missing out on the opportunity to build in one location out of three... that's just not fair. Beth needs to fix this ASAP.