OK. If you do not mind. Let is just start fresh again. Make sure you follow all the steps below.
1. Go to stecnylworks/games folder under User Document and save all your games to a personal folder.
2. Make sure you have admin priveledge as a window user.
3. Note that if you use window installer to download sw, you will see two areas of sw.
a. You should see Stencylworks folder under Program files. This is the program executable of sw.
b, You should see another Stencylworks folder, .stencylworks folder and stencylwork.prefs under User Document. This is mostly the data files and game centric files.
4. Manually remove all of the above.
5. Now come here and install with the window installer version (second one).
http://community.stencyl.com/index.php/topic,3874.0.htmlThe whole database should be a little over 50MB.
6. After installing, you should see all the files/folders that I mentioned in 3. .stencylworks may not be there under user Document but that's OK.
7. Now make a quick game and test if you are still losing scenes or resources.
8. Anytime you add a resource like actor or tiles, you should see it under:
User Document/Stencylworks/games/<your_game>/resouces
Hope this works out.