Rene,
After the initial clone the behavior stopped, but because it started back up again last time I decided to wait a day before saying it worked and unfortunately this morning TeXShop has started opening again.
I do not know the difference between a compiled applescript and an uncompiled applescript. There is still just a file, refresh_viewer.scpt, no application or anything like that in the bin directory. Could my textmate have updated itself back to the uncompiled version? How do I check if this script is compiled or not?