The film was re-rated because GL resubmitted it. I think it was a smart decision on his part, since the meaning of the PG rating has changed significantly in the last 34 years. PG ratings used to carry a warning in the rating box stating that the content my not be suitable for pre-teens, and many films rated PG by the MPAA got much stiffer ratings elsewhere. I honestly think that GL may have been concerned that some people would think that a movie with his name on it, carrying a PG rating, is suitable for viewing by unsupervised children, which is clearly not the case with THX-1138.

Re-rating is a funny thing, though. If Planet of the Apes (1968) were resubmitted, it would quite likely get a PG-13 (current rating is G) for roughly the same reason as THX got an R: nudity. As well, when The Wild Bunch was recut to the director's specifications in 1998, it was threatened with an NC-17 if it was resubmitted. Warner got around this by using the rating that was originally given to the DC in 1969 (yes folks, that's right: both the theatrical cut and the DC had the same rating). Funny how that works.