This problem is still here and yes I'm using 4.0.0.5477
Now when you hit Save As and write to a new file it makes the new file, but subsequent changes are NOT SAVED to that file. They aren't necessarily saved to the previous file either. I just did a test opening a file named 006.ttr, saving out a file named 007.ttr, then making some color changes and hitting the save icon. When I closed TT and looked at the files the changes were NOT saved to 007.ttr, NOT saved to 006.ttr, but WERE saved to 005.ttr which I hadn't even opened during the previous session. This needs to be fixed immediately as anyone who is working with this version could be writing over old files without even knowing it. I do NOT recommend working with this version.
This is easy to reproduce just open a blank wordpress template, save it as 001. Then save as 002, make some changes and hit save. The changes will be applied to 001 and not 002.