I have WebJCS up and running, but I'm having trouble saving the level after making those changes (the progress bar stays empty while trying to save it, and only Save As... and Run can actually be used, the latter also causing the saving loop), so I can't actually test it. Any idea what may be causing the problem?

EDIT: I've attempted several different methods of getting WebJCS to work, mainly by moving it to different locations and changing settings in the settings.ini file, and all the results are still the same. It can find all the levels and tilesets present in my JJ2 folder, but it keeps getting stuck when attempting to save a level (the progress bar stays empty, but the animation just above it works properly). I'm also using Windows 7.

On the other hand, I do see what you mean by using an animation as the first frame of another animation. Once this issue gets resolved somehow, it will be interesting to see if the Destruct Scenery event animation functions properly using this specific method.