Layers disappear when saving in CS6

My layers disappear when I try to save in Photoshop CS6. They disappear when I get to the last step before saving(where you can select the quality and stuff). The effects stay, but they become kind of crappy. I've no idea how this happened either. I was just working on some pictures one by one, and then suddenly, it started happening. I did nothing differently.
Reinstalling didn't help either. What the hell is going on?

You're seeing normal behaviour/results. Most image file formats do not support layers and there can be subtle to huge differences in the display of a layered doc versus its flattened composite because Photoshop uses imprecise shortcuts to generate the composited display of a layered doc. The display discrepancies can be minimised by viewing at 100% zoom.
While working on a document, check adjustment layers, effects and layer blending with zoom at 100% so there are no nasty surprises lurking in the doc. (Of course, I realise that there's a very good chance that you may be viewing only a small region of an image when zoom is 100%.)
Regarding the JPEG save in particular: when you are at the stage of picking quality/compression, there is an option of previewing the result of the compression. JPEG doesn't support layers, hence the flattened composite at that stage. Your open doc will still be layered after you commit the save.

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