I have a Samsung GS2 T989 and had the same issue. It came to a point thatit would simply beep and disconnect itsef.... tried different solutions:
1) initially, I gave up on using the charger and purchased new batteries. Got a set of two plus wall charger (http://www.amazon.com/Hercules-T-Mobile-Skyrocket-18-Month-Warranty/dp/B0078WL4YO). LOVED THEM!!! With two batteries, I had no need to use the usb charging
2) still tried to use the "half dead" samsung battery- simply charging it on the Anker charger instead of using usb port
3) worked for a while, but then started having issues in synching the phone to PC - USB was really gong south... so I reset phone. After restoring to factory settings, the USB port is now working 100%
good luck guys