its best not to use the usb, use a desktop charger and ssh to transfer data that way your at least minimising any potential problems with usb port, lol maybe that may not be enough.LOL
My usb final broke off completely. Simply don't need it anymore.
I bought 2 extra batteries and use my old defunct N96 to to charge the BL-5J battery. They battery doesn't need to sit flush, just clip in an touch the prongs.
With 3 batteries, i am able to use the N900 continuously.
I had this problem, stop charging PLUS won't start if not in R&D mode. I reflashed like 8 times, it wont'charge. I had to buy and spare charger and batterys. Like you said, the usb works for transfering data, but charging is what stop working. I want to try to dissasembly and try to see if I fix the usb but maybe I will make it worst, so.. Space charger and battery it is!