Now regarding those issues, I don't know pretend to know anything about this situation, but in some cases "unresolved rights issues" really meant money was the issue, however I really don't see this very obscure film, with now almost-equally obscure stars, as being much of a moneymaker in 2014.
If you're suggesting TT is covering dropping this title by fabricating the rights issue as a more excusable pretext because the company second-guessed, I seriously doubt it. It's more likely that when TT announced the release of this title, Fox's lawyers discovered that there was a snag in the rights somewhere. I suppose it's possible, but TT is known for taking risks and if they seriously doubted this title, they wouldn't have bothered with it in the first place.
A similar thing happened when the Fox film Boomerang was first issued on DVD and was pulled at the 11th hour. They eventually fixed that pretty fast and hopefully they do the same here. Though that was more of an exceptional case since Fox had already spent thousands of dollars manufacturing the DVDs (some of which leaked to the public) and distributing them to retailers beforehand and was more anxious for a return on investment, even at a hefty price. Centennial Summer, on the other hand, shows no signs that it has gone as far as disc replication or even getting the cover art finalized.
I think this case is somewhere along those lines--since this film is (or was) being released after being ignored by Fox for so long, their marketing lawyers double checked this title to ensure no lawsuits would arise from copyright and indeed discovered a discrepency that had previously been overlooked. Since this is a musical, the most likely reason was that there was a song (or songs/portions of music) which have not been cleared for copyright or that Fox lost the rights to over the decades. In this case either Fox will resolve the issue or it will become (temporarily or permanently) insurmountable, be it too steep of a licensing cost, the copyright claimant is non-receptive, or other reasons.
Centennial Summer was based on a 1943 novel by Albert Idell. The most common legal complication for films based on other works stems from the case of Stuart v. Abend (http://en.wikipedia....tewart_v._Abend), where the issue is whether the owner of the film has the rights to distribute it where someone else owns the rights upon which it was based. I would have thought that Fox would not have licensed this film to Twilight Time if there was this common of an issue with it, but perhaps not. On the other hand, perhaps there's some odd isssue with the music or something.
If it's an problem with the author's family or related copyright holder, it's a pretty bad sign. If they haven't budged in the past, there's little chance they'll budge now. Fingers crossed that a) this isn't the case and b) a compromise can be reached.