Beam core engine consumes vastly more hydrogen than antimatter by mass.

[MutatedRaincoat]

The beam core engine consumes equal units of hydrogen and antimatter per second, but they don't have equal masses. 1000 units of liquid hydrogen weights 71 kg, and 1000 units of antimatter weighs 10 kg, according to the Kerbal Engineer Readout.

[JadeOfMaar]

This ratio is copied from the FFT BCAM so this problem first exists there. My interpretation of the issue is that Antimatter (by lack of density) is equivalent to Positrons but BCAM is described here as requiring AntiHydrogen (including/using the anti-proton), which does exist in the CRP and has a proper density value.
I've planned long ago to fix this but with it is my intent to deprecate the existing part and replace it with two or three new and hopefully better looking ones and use the AntiHydrogen resource.