PPCGeeks - Wierd ADRYN 3.0 issue... My Storage\Program Files... gone?

So earlier I did a soft reset on my phone, and when I went into the start menu I noticed that a bunch of programs were missing their icons. All of these programs would no longer work, and they were all installed to My Storage. I opened up file explorer and went to My Storage, and everything was still there, except inside the Program Files folder... everything was gone. I thought weird. So I try to reinstall resco explorer, it tells me there is a version already installed and I have to remove it. I click yes, then proceeded to reinstall it to My Storage. It finished installed, I go to start, it's all the way at the bottom since I just installed it, but has no icon. Doesn't work either. Go back to file explorer, and check my Program Files folder on My Storage. Nothing is there still. Anyone know what is going on?

I am running Adryn 3.0 and have been since it was released with no problems.

My only idea is to backup what I have on My Storage still, and format it, and copy everything back and reinstall my programs.