(Java) Timer objects 'running slow'

Hi. I have a java game I made in a course at Uni. It has three Timer objects.
When I run the game from Notepad++ it runs perfectly (sweet-as game if I may say so myself).
I have made executable .jar files so that I can share it with friends. Unfortunately sometimes the game runs 'slow' when run from the .jar.

I have the feeling this has nothing to do with errors in code (due to the randomness of the error's occurence) but rather a runtime problem (if that's the right word..).

Anyone know what the problem might be?
Also plz keep elitism to a minimum

>>27
Yeah that's pretty anal. Most of the A3Constants class was provided with the assignment. I added a few things in there.
>>29
Thanks for the suggestion. My hitbox system is quite roundabout - there's a box 3/4 of the player, as well as a Point on each extremity of the player - The box or points make contact with the box of an enemyball (which are simply boxes around the circles). From all the playing I've done I haven't noticed any obvious false positives/negatives. Of course they're there, but in those cases a collision would happen in the next frame so it's not noticeable.
>>31
The enemyballs direction/speed is randomised every time they disappear. So the intial pattern is quickly broken, there is no 'safe spot'. I quite like the effect of them all starting in the corners.