Pre-amps will make your recordings darker or thinner in certain frequencies, but they shouldn't make it 'boxy'. The 'boxy' typically comes from the room mainly, the effects, the distance from the mic. It may be that the pre is better at getting the whole spectrum than the stock one. Think of it like a telescope. A better one will help you see more stars, but they were there all the time. Obviously, though, if one pre is magnifying unflattering aspects of your room, take it out or treat the room. In the end, you've got to make it work the best you can with what you've got.
If you don't believe it, you can do a test. Hook up your mp3 player or some other noise maker to your pre and then listen to the output. Does it sound boxy? If not, then your problem is in the room. If it is, then the pre or something else in the chain is the problem. Good Luck!