If you are switching to "Draw Box around current line", which I HIGHLY recommend, you will need to turn off "Current Line" coloring for Java. To do so, go to Tools > Options > File Extension Setup... Select "java" and switch to the Advanced tab. Under "Color Coding", uncheck "Current Line". You may also need to do this for other languages you had enabled Current Line coloring for.
Unfortunately, the "Current line" color coding is heavy handed. Ideally, it would only effect the background color. We are looking into improving it in a future release of SlickEdit.