Current problems with Buck-Boost Lipo loader evaluation board
The 2.2 ohms you have added reduces the inductor's ability to extract energy from the incoming supply quite significantly and therefore, your buck-boost circuit has to take more current (i.e. operate at a fatter duty cycle) to provide a stable voltage at the output under its load conditions. Try using something much lower like 0.22 ohms or 0.1 ohm if you can find one.

Another problem is the way you have used the o-scope to get the picture of the voltage waveform across the 2.2 ohm resistor. Oscilloscope probes are not floating differential inputs and, in effect, you have grounded one side of the resistor with the wire attached to the o-scope probe. It's hard to say how much this affects things but it doesn't help.