No, you’re not the only one. I am having the same issues that sometimes, “show in Finder” commands issued from other applications open the new window under the top-level window of TF. I cannot provide a 100% way of reproducing it, which leads me to believe that this might be a timing issue. Just for the record, I also use TotalSpaces.
From the description, this issue looks similar to the one described here.
– kriro