I suspect, you used some internet connection "tweaker".
Is your computer clean of bad guys now?
so I deleted it
Do you mean, uninstalled, or just deleted.
If I changed something using a program and then deleted the program do the changes stay or are they also deleted?
It depends. If you UNINSTALLED that program, if it was a solid program, it would ask you, if you wanted to reset your settings to how they were before. If it was a lame program, or if you just deleted that program, changes stay. And it looks like it's your case.
I'd like you to run TCP Optimizer from here:
http://www.speedguide.net/downloads.phpIt'll check your settings, and it'll try to correct bad settings. No guarantee, but worth to try.