Errors when minimized

I've noticed that Gilgalad will sometimes throw a lot of ArrayIndexOUtOfBounds exceptions at the start of the first round when I pause robocode, hit restart, minimize, and unpause from the "Gilgalad console" window. However, it never happens if I start the battle from robocode, and then minimize it. Also, I saw some strangely low scores against Raiko mini in local tests (one as low as 15%) which may be related. I'll try to test on different JVM's, OS's and machines in the next few days, but I was wondering if you had any idea why minimizing the robocode window would do this?