Unplayable on Firefox on Linux at least on this machine/my settings but looks like a lot of effort went into it (I get to the starting screen with the space ship and a shield bar which already has a red bit and then it doesn't do anything more)
In the game press the [Esc]ape key to pause and get the menu (then the menu works and you can return to the main menu) however if the game loses focus (mouse click off screen) you get the same menu but can only return to the puzzle.
GsusAD I use the save button in Options and that works for me, haven't tried using Ctrl to save yet. It could be that your browser (or a plugin) wipes your (flash) history? Use a search engine to find out more about that.