Since the latest "update" to Photoshop CC, I cannot use the Save for Web feature for some of my files (files that worked just fine prior to the update). When I try to save out a flattened image, using Save for Web, most of the layers are missing - as if they are turned off in the layers palette (but they're not - they're on).
I called Adobe and spoke to a rep who would listen to my issue, put me on hold, then come back and ask me to please describe the issue again. After the third time, he said he was going to transfer me to someone who couple help. I then waited on hold for another hour and 20 minutes before I finally hung up.
Hence my comment about the awfulness of Adobe's customer support.
Ok, I am not experiencing this problem, but I'll throw in a few ideas.
If you are up to doing this, hold down Ctrl-Alt-Shift keys while starting Photoshop to reset Prefs.
It's been known to clear up irregularities.
Maybe a complete uninstall/reinstall is best.
If you don't want to, you can try Image > Duplicate, then Layer > Flatten Image then try SFW.
If you have a folder of these layered images, you can try File > Scripts > Image Processor which can batch convert your files to jpeg.
I know Phone Tech support can be bad, but if you want to... try again, you may just get the right tech.
If you are offered a callback, take advantage of it and they will ring you back when it's your turn.
You can also try Google to see if others are having this problem and see what they recommend.