Certain things are not fully compatible with certain browsers. It's likely that the KTSY page or another that you use every day is the culprit; it doesn't "like" Safari for some reason. You might try another browser, such as Firefox, Chrome, or Opera. You could use the other browser just for KTSY and continue to use Safari for everything else.
It's very unlikely, but some component in Safari could be missing or damaged. You might try installing the last combo updater (link below). Repair permissions before and after installing the combo update.
You might consider getting in touch with KTSY and reporting the problem to them. They might be able to replicate the error and then work on a fix from their end.
Finally, consider just putting your Mac to sleep at the end of the day and waking it up at the beginning of the next working day, instead of shutting it down at the end of each day. This will not use much more electricity, and you can pick up exactly where you left off with no waiting for shut down in the evening or boot up in the morning.
I will try that. Its probably KTSY that is causing Safari to throw up. But it does seem weird that I cant go in and quit Safari. And also that when it opens up, it opens up all these blank windows.
But I think part of the problem is that I use, what is called Full Screen mode. It looks like Full Screen mode is still pretty buggy. When I dont use Full screen, things seem to work better.