how did you preprocess your images in Lightroom? preprocessing in astrophotography generally refers to the process of calibrating images with darks, flats and bias frames. LR can't do that...
anyway, seems like your problem is with LR? maybe you have exported the images without the LR adjustments?
IMO you should just use PI to do everything, but generally speaking if people use PS or LR they use it at the end of the processing pipeline, not at the beginning.
rob