just tried the new update and I Think I discover some bugs and got some questions.
The first thing I noticed when I went to the scene designer is that some of my actors are flipped.
Here are some screen shots:

As you can see the spikes are flipped horizontally
Hey just a heads up, but I've made it so Stencyl fixes this automatically coming from 2.0 or earlier versions.
If you fixed this manually using 2.1, you might have to rotate this again. If you are familiar with XML editing, you can prevent the actors from being automatically rotated by changing the "format" attribute of the scene's xml file from "1.0" to "2.1" (In your scene folder, you'll see a listing of scene xml files in the format of 1.xml, 2.xml, etc...).
If you went back to using 2.0, you shouldn't have to do anything if you didn't save that scene in 2.1. I could also adjust your scene files myself if you aren't familiar with XML editing and don't mind sending the game over PM.