I'm not sure the real reason why, but my LCR meter, the higher the frequency I test at, the lower it reports the capacitance. So that doesn't sound too weird. I'm sure I've measured 100uF caps at 100kHz, and the meter, however it calculates it, would say 10-20uF, or something like that for larger caps. But at low freq, allowing it to charge, like with a DMM, they would read within tolerance, which is often like +/-20%.
So I usually ignore it, and just go by the ESR at 100kHz, and dissipation Factor at 1kHz (or 120Hz for that I can't remember)