Hi Ironsniper, welcome to the forum! A dedicated LCR meter (I haven't got the DER5000 but an Applent AT826, yet for practical applications they should be comparable) offers many parameters that may actually affect the measurement results. First of all, it's always a good idea to use kelvin (four-wire) probes to measure the voltage directly at the terminals of the DUT and eliminate the resitance of the probes/connections themselves. Moreover, the measurement frequency has a major effect on the results. Especially electrolytics will show a considerable dependency while small plastic foil (particularly polypropylene/polystyrene) caps are almost independant. In case of the electrolytic caps, the temperature of the DUT also may have considerable effect, though this affects more the ESR than capacity. Electrolytics are usually specified at 120Hz measurement frequency, so please make sure you select something in this range.
Cheers,
Thomas