Check the basics, is the cable plugged in properly, check the resistance of the cable, are you noticing it gives the "?" when using a specific cable, and not with another cable.
The problem you describe sounds symptomatic of your "high capacity" battery not presenting the appropriate configuration data or data-pin setup to the device to indicate that it is capable of supplying more than the 500mA standard for USB and so your phone is falling back to 500mA only.