For some reason LimeWire always starts up when I start up the computer and log into my account. It really slows things down and it takes forever for it to be able to let me to close it off. Is there any way I can change this? I thought I changed it in the options menu but it doesn't seem to have helped. Any help is appreciated, thanks in advance!

Tools > options > advanced > system startup. Untick 'run on system startup' > apply > ok.
That should do it

Once you've shut LW down, does it keep on popping up by itself? If so, that's a virus
WARNING: Viruses on the network you should be aware of

That box is unchecked and it still comes up on startup.

Does it keep popping up after you've closed it, or is it only the once on startup?

If it's only the once, try deleting LW's preferences folder when LW's properly closed. See points 2 & 3 below for instructions
Fixes for LimeWire
If you've used older versions of LW before, you could have a preferences folder in the location mentioned on point 2, or as mentioned in point 3...so check for both. Remember to show hidden files & folders. After deleting that folder, you'll have to go back through your options & reset everything to the way you had it.