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I just jailbroke yesterday, and am having this problem. Installing or uninstalling anything from Cydia will make the icons come back. I've uninstalled all tweaks that is installed since I noticed it, one by one without success. Only have Winterboard, iWidgets, iFile, Bytafont 2, FlipCC, Activator (required by FlipCC), SwipeSelection and zeppelin installed. Last tweak uninstalled was CustomLS. Everything's back now, and it didn't happen on the last theme change, so I'm hopeful.

Any permanent solution, though?

Edit. Nope, still broken. Can't install from the Apple App Store either. Done with this JB I think.
 
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After restoring this morning to solve an issue with the App Store, I watched the tweak install as I added things. I had disappearing icons as soon as I installed Winterboard (before even applying a theme) and have had no issues after removing Winterboard, even after adding many more tweaks.

So, at least from what I've seen, Winterboard appears to be the culprit. I'll stay theme free for a while and hope Saurik fixes the issue.
 
I am having this issue as we'll with batterylife, flex and ifile. Those are the only ones I notice because they're the only tweaks/apps I have that aren't completely hidden and I can still see the app icons in an activator menu.

If I reinstall one of them it brings them all back, but it is really annoying. I am getting this on my newly jailbroken iPhone 5s, 7.0.4.
 
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