If i was you i would recreate the logo with a transparent background, this would alleviate that from happening. If you are unable to recreate it, instead of using GP Studio to remove the backround, uncheck the print black ink option in the print window. However, you will not get any black ink anywhere on the design which you might want since you are printing on a blue shirt. In which case, your best bet might be to recreate it with a transparent background, which is what I would do.