I own a B1XON and a Squier VM Jaguar Special (PJ) and have no problems with boominess when using headphones. I also don't have any custom patches, just what was programmed straight from the factory; though I do notice that the overall level (volume) on some patches is definitely louder than others. If I had to guess, maybe your bass is too hot/boomy on the low-end?
sleepy
sleepy