You do not need Catalyst to run at startup. Its simply useless, adding to the boot time.
Press Windows flag key+R and type msconfig in the Run box and hit enter. Go to startup tab and uncheck items related to catalyst.
Now, coming to the double icon. That doesn't seem a big deal. I too sometimes face it not only with catalyst but with other icons too.
I can't say why its so but it doesn't affect anything.
You can still try rebuilding icon cache and see if its gone. Icon Cache - Rebuild