Thanks for the response! I had the computer on for about 12 hours yesterday to let it hydrate as you said, I haven't touched anything as far as "Fast Startup" but should I?
Twelve hours should be plenty. I would definitely turn off Fast Startup, at least for a while; do some reboots, see if there are any updates in WU, etc. Do you know what Fast Startup is/does?
To understand what this is/does (it was first introduced in Windows 8):
“Fast Startup (aka: hybrid boot or hybrid Shutdown) is a new feature in Windows 8 to help your PC start up faster after shutting down. When turned on, Windows 8 does this by using a hybrid shutdown (a partial hibernate) method that saves only the kernel session and device drivers (system information) to the hibernate (hiberfil.sys) file on disk instead of closing it when you shut down your PC. This also makes the hiberfil.sys file to be much smaller than what hibernate would use (often 4GB or more). When you start your PC again, Windows 8 uses that saved system information to resume your system instead of having to do a cold boot to fully restart it. Using this technique with boot gives a significant advantage for boot times, since reading the hiberfile in and reinitializing drivers is much faster on most systems (30-70% faster on most systems tested). If you have a motherboard with UEFI, then fast startup will be even faster.”
Unfortunately, there are some times/things that just need a full, real shutdown to get right. You can always turn it back on any time.
There's only a handful of apps that don't show up so I figured they were being installed into a incorrect folder that won't show up. The apps that are not showing up are game clients like Origin and Battle.net, everything else seems to show up fine at the moment.
I have both those games installed on my system and they both show up in the Start Menu. They were installed on version 10240 - the first General Release to the public about a year ago. So, I'm not sure why they would not install correctly for you - doesn't make sense, you know? But, the games are working correctly?
All the store apps show up (even though I don't use them) it only seems to be apps that I install that go missing. I've also done the scans and repair install that you mentioned and they see the PC as healthy with no problems, so I don't know what to do from here.
If sfc /scannow returned "no integrity violations found", and CHKDSK had no repairs to make, that's good. You also did a repair install?
The next thing we can do is manually place them in the Start Menu. Not really a solution, but it will accomplish the goal. You game?