The "only" thing that's changed is your ISP? Changing your ISP changes a whole lot - are you sure your connection isn't just slower now?
In any case, what's being slow? The actual transfer times, DNS lookup? A flash cookie would be, appropriately, only read by flash. They're just little files, they can't hurt you.
As for viruses, while they can hurt you, very few are built to cause you serious issues. Best case for a virus is that get gets in undetected and is then able to do what it wants - making it obvious it's there defeats the point. Contrary to popular belief, a virus is unlikely to seriously impact system performance.