I am running Version 1.0.2 (v20) of Skim, Version 1.5.7 (1455) of TextMate, Leopard (10.5.1). I could give you a file if you want, but all you need to do is have two distinct .tex files with the exact same name and in different directories on your computer. Have both of them open in TextMate. Compile one and it will show up in Skim. Compile the other and it will think that you're trying to update the first file that you compiled because they have the same name.
Keith