First: After I installed the Avast when I now start up my computer it loads the folder my documents along with the other 40 things that load and it's annoying. how do I make it stop...?
That isn't avast doing that but windows. If you happened to deleted some malware when you installed avast, there could be a run command for that process, if windows can't find the file for some weird reason it opens the folder the file should have been in. The trouble is trying to find what that was.
Can you give examples of these 40 things ?
Second. ok under the scanner sensitivity it says Instant Messengers: - MSN Messenger - ICQ - Trillian Messenger... ok but the only messengers I have that I know of are Yahoo and ICQ. I have no clue why the other two are showing up... am I missing something...?
Click the Details button on that display screen, it will open things up go to the Instant messaging and click customize, you will now see a list of all the IMs that avast supports. What you saw in the initial screen is just the first few of those, if you want you can uncheck the IMs you don't use.
The same is true of the P2P Shield.
Also when I run the scan it takes like two hours to scan the following location D:\Inetpub\mailroot\Badmail I go there and there is nothing there so why does it take two hours to scan that folder...?
You don't say what the type of scan nor sensitivity you did, a thorough scan with Archives enabled, which I think you tried will take a long time. Though two hours for a single folder no matter how large seems wrong.
You don't say what the system is, what windows version, CPU, RAM, etc.