For some reason USB ports 1-3 on my ps3 will not recognize or charge a six-axxis controller, but usb port 4 will. What I was wondering is what could possibly be wrong because the usb ports still work for things like USB Flash drives, USB keyboards, USB MOUSE. They just won't recognize or charge a six-axxis controller!
Try switching of and removing power cables from your PS3 for a couple of mins and then connect and try again. Could be your ports just need to be reset. other than that call Sony support cause if you having issues with power levels in USB ports 1-3 .. 4 should start seeing it soon too.
I use my Razor's charger to charge my Six Axis as i have a wall socket right next to my couch and dont need to sit close to the system while playing and charging