This line here is the reason why we kept using Java's standard regexp api. Because jRegexp take the string and converts it directly into a char array. So if a  bad and long line with a lot of exotic characters gets put into this matcher it can stay here matching the same line for hours, so we needed a possibility for a timeout. 
Perhaps I should have put that in a comment somewhere during my investigation :)

Can't you provide the same features with the standard regexp API?