It seems setting the bottom layer to a parallax other than 100,100 results in screwy mouseX and mouseY reporting.
I assume this is a bug, rather than some weird feature that allows you to parallax your mouse - because I can't think of a way to use this for anything other than disorienting the player.
These 2 caps are identical aside from the parallax setting on the bottom layer. The ship is supposed to point toward the mouse, and move toward it when you hold the left mouse button. It works fine in the first example, but gets utterly confused in the second.
Default parallax of 100,100
Parallax set to 25,25
As far as I can tell, this only happens when changing the parallax of the bottom layer, not of any of the other layers.
Oh, and I'm using release 63 (64-bit) on Windows 7, if that's helpful. Let me know if you need any other information, or if the caps don't do what I described.