A few terms.
http://en.wikipedia.org/wiki/Ripple_%28electrical%29
Ripple is a periodic variation of DC at a the fundamental or multiple of the fundamental. In a full wave rectifier it is 120Hz. In a switcher it could be 10kHz to maybe 1MHz.
http://www.tvss.net/trans/trans-x.htm
Transient voltages are random and often caused be switching inductive loads.
A capacitor of the correct value and type placed in the correct place will help to eliminate both ripple and transient voltages.
LED flicker may be caused by a random fluctuating voltage, bad connection, bad LED, bad convertor, or other things that are slowly fluctuating. Ripple on a LED at 120Hz can not be seen with your eyes even though the light is varying.
A slow fluctuating voltage may not be filtered out with a capacitor depending on the amount of current drawn and the length of time between fluctuations. The battery is a good filter at low frequencies, not so much at high frequencies.
Putting the LED across the battery with the power on may tell you that the converter is bad ( a volt meter may help also). It may tell you that the LED flickers with the higher voltage at the battery from the converter. If it does not flicker then wiring to the filtered output of the converter may fix the problem. Anyway it is just another test to help narrow down the problem.