Uh... 90mb is massive, you could have stripped that down to a few mb easily. :V I´m not ever going to find anything in there, that´s exactly why Ashley always wants minimal repros for bugreports. You can get rid of all the non-relevant parts: layouts, event sheets, graphics and especially sounds/music. Also has the benefit that nobody can rip anything of value from it then. (On that note, you have the copyright anyway. If you see someone using your stuff, an angry letter from a lawyer usually solves that really quick.)
One thing about the screen shake is that it doesn´t work when you are at the edges of the layout. It´s a quirk of that particular action (it´s uses scroll but isn´t allowed to scroll past layout edges).
About the minimap dots not vanishing... no idea. If you can strip down the project much more it will be much easier to find the issue.