Why are half my textures unaligned now?

[Snikle]

I opened up Doom Builder today, and like half the textures on my map were unaligned, even though they were painstakingly aligned beforehand. Like all of this used to be fucking perfect, and now it's like this. Was it some Doom Builder update? Is there a way to fix it other than spending a day realigning it all?

Note the switch, the computer panels on both sides, the lightbar on only the right side, the bar above the whole switch assembly. Even the rocks were already aligned. What happened?