Why are apps disappearing after I install them?

I am new to Ubuntu (and Linux in general). I installed Ubuntu 13.04 (after many installs of 12.04 and failed Office installs even though the web swears it's possible). I gave up on getting Office installed.

Anyway, yesterday all of a sudden I noticed Ubuntu Software Center was gone. So I rebooted. Then, upon logging in, I had a blank desktop. Thankfully I left Windows 7 installed on a separate partition so I logged in and Googled it. I ended up finding some info about booting up, invoking terminal -- but wait, Ctrl+Alt+T didn't work anymore either! :(

Booted Windows 7 back up and Googled THAT. Found info about ccsm and also unity --reset. I booted back into Ubuntu, managed to get to a terminal by using Ctrl+Alt+F1. I typed ccsm and it said that wasn't installed.

Back to Windows 7. Google. Found info about resetting Unity by doing unity --reset. Then read that was deprecated and to use replace. Then read that was deprecated too. AHHHH! I decided to just boot Ubuntu and try things people said WEREN'T possible, because I had the notion that anything I read that WAS possible wasn't, and vise versa.

Booted into Ubuntu, ran unity --reset and it told me Unity wasn't installed. Thankfully, it said: to install just type sudo apt-get install unity. That worked, and, upon reboot and logging in I now have my desktop icons -- or should I say that left panel thingy. Ubuntu Software Center was still gone but I was able to install that via another command...even though I used to have it already.

Finally, to my question. How does stuff just disappear? Did my Ubuntu install somehow roll back? I don't remember uninstalling anything to make a lot of built-in things just disappear. I installed Guake (the transparent terminal) and now that's gone too. When I install stuff, is it installing it to a certain shell? Session? When I press the "Super Key" (the Windows logo key) and type term, I no longer have the built-in terminal app. Huh?! But, I have UXTerm and XTerm -- both apps I never saw before when I searched for "term" in the search...thingy.

Ideas? Insight? Anything would be helpful at this point. I LOVE Ubuntu and I'm glad I installed it. NOT going back to Windows.

Thanks!