the 2 capacitors are for to stabilize the charge
they can create a disturbance to the line ,
what do you mean with checking the jumper? it's a filter, check with tester / multimeter if has continuty , if no desolder and jumper.
another possibility from noise could be charging line so replace dock ( can to be in short) and in sequence ,carefully replace usb charging ic (u2) 1608A1.
usb meter I warmly recommend it costs little and helps a lot
