Your save code's looking pretty solid there! You do seem to be checking for events on animated tiles now, you're calculating DoesLayerHaveAnyTiles on saving, and it looks like you're even counting flipped tiles (even within animated tiles), even though that section of data1 was only added to the wiki yesterday. Fast work! Issues I've noticed so far:

• In JCS, if your selected tiles come from the tileset, the blank tile (0,0) will always paste, even if you're not holding down shift. You only have it paste if you're holding shift or if it's the sole tile in the selection.
• The "saved files" list seems to have some sort of maximum length, since it only gets as far as R.
• You don't do a password check.