The game is full of bugs, but I playtested it many times and never encountered the ones you describe.
The purple enemy in the jump power-up room is resistant to normal bullets, you have to beat the first boss to acquire the charged shot and kill it :)
As for the size of the window, there is a delta of 10 pixels. I don't get why, but this seems to be a Java thing. Instantiating an x * y window causes a x+10 * y+10 window to appear. I had to account for it.