According to asosbrigade.com, the ASOS Brigade site run by Bandai:
The Regular Edition DVDs contain the exact same episode order as released in Japan on the R2 DVDs. [...] Due to pre-existing contractual obligations, the regular edition MUST contain the R2 DVD ordering of episodes. This was set in stone, there were no exceptions. [...] After deeply intense negotiations to try and please the existing fan-base, we are able to release a Special Bonus DVD in the TV Broadcast order as an extra.
According to a DVD 1 review by ANN (May 31st, 2007):
Another oddity came in the fourth broadcast episode, which originally jumped ahead to episode 7. This DVD release does not do this, however, instead opting to release the episodes in chronological rather than the scrambled broadcast order
According to the episodes list on ANN, the broadcast order against chronological order is:
Broadcast 1 2 3 4 5 6 7 8 9 10 11 12 13 14
Chronological 11 1 2 7 3 9 8 10 14 4 13 12 5 6
This order is reported in the episodes list on Wikipedia as well, with DVD release following the chronological order with the only exception being the first episode.
asosbrigade.com reports the chronological order (C) as Haruhi's order, and the broadcast, "scrambled" order as Kyon's order (B). The Regular Edition DVD order is Haruhi's order, with the exception of the first episode.
Regular edition was and ever was in the right order because of "contractual obligation": Region 2 DVD (Japan) must apparently have the same content of Region 1 DVD (USA). Bandai was pressured by fans to release the "scrambled" version.
Why did they have to, back in 2006-2007? From here on, speculations: because fanbase watched the fansubbed version from the broadcast (2006-04-02 ~ 2006-07-02) and ask for that order. I cannot find evidence of requests by fans to do so, so we have to trust Bandai's words in the meanwhile.