Some of my programs are no longer in my start menu. Could this a virus?

Obvious programs where missing, such as Firefox. But I could still search the computer files and found it in its own folder. But then programs I didn't use often are missing are missing and I can't remember what they are, but I know they are gone because I used to have to scroll down in the menu to open a favorite program.
I've ran two different scans in Avast and nothing come up wrong.

The one thing that I did differently then usual was try to download a Minecraft texture pack that didn't work in Chrome, so I downloaded it in IE. Around that time Avast said it caught a virus, but I was to absent minded at the time to pay mind to it. This is the link http://www.planetminecraft.com/...naissance/
(I scanned the download^ and it came out clear)

Please help! I'm really worried, if can help I would be so grateful.
I'm restarting my computer now to see things get worse/better. This will be fun.

That site has 6 trackers on it (spyware), so do a scan with free malwarebytes & free superantispyware & see what they remove.

No problem!
For programs simply right click the program and from the menu you will see the option to add it to your start menu or even your task bar.
For a list of programs you can't remember go to "Control Panel" and open "Programs & Features".
From there you will see all your installed programs.
Then type these names, one by one in the start menu search box. The name of the program will appear in the upper portion of the start menu. Again right click and choose "add to start menu"
Only problem is that you have a limit how many program names can fit in that are visible. Scrolling will reveal the ones that are not instantly visible. Sometimes programs accidentally get taken off. Also this is how to delete programs from the start menu. Right click > choose remove.
Also you can left click a program and drag it to where you want it on the start menu