Pretty Links Clicks are way higher than other tracking solutions?
Be sure to enable the Filter Robots feature in Pretty Links -> Options -> Reporting page. Robots are constantly trolling websites, enabling this option will prevent known robots from being counted in the Clicks. This works best if the "Extended Tracking" Tracking Style is enabled as well.
It's also a good idea to add your own IP address (whatsmyip.org), and the IP address of your website (whatsmydns.net) to the IP Excluded IP Addresses setting in the Options. If you do these things they will prevent Clicks from being tracked from these sources to further prevent skewed Click reporting.
Because each tracking solution uses different filtering methods, it's unlikely the numbers will ever perfectly match up, but doing the above will help to bring them closer together.