I am surprised to admit it, but I think I've finally found the space horror campaign setting I need and its name is Septimus...sort of. Here's the thing, the Septimus game setting, as written, is more space opera than space horror. However, with some tweaking, it could easily be worked into the game I'm looking for. It has two things going for it, one crunchy, one fluffy. The crunchy bit is the d6 system. Recall, when I first went all delirious over Fading Suns, it was the d6 system I looked to for my conversion. I still think d6 is the best for gritty, realistic sci-fi. You don't want high-level d20 demigods stomping around in your space horror sandbox, routinely beating the snot out of your "Horrors-from-Beyond-the-Stars". There has to be real fear there to make it work.
The fluffy bit is that Septimus (the place) is a prison, a very large prison to be sure, but a prison nonetheless. Anything going in is not getting out. Therefore, to really scare the pants off the players, you can trap them inside with something big and bad. Combined with the technological horrors being unleashed by the Extent as it thrashes around in the aftermath of Steel Helix and you have all the ingredients for a pretty intense space horror campaign. Septimus is a big enough sandbox such that you can run for awhile, but ultimately, there's no place to hide.
Further note: Septimus and AT-43, beautiful synergy there.