The 'eject waste now' button on the reactor control screen (visible only when autoejection of waste is turned off) ejects the entire contents of the reactor, converted into fuel, out of each input/output port when pressed.
The following methods of ejecting waste/fuel are unaffected, and function normally:

• Item I/O Port fuel/waste eject buttons.
• Rednet waste eject signal.
• Redstone port eject signal.

I was not able to test the eject function of the computer control port, as computercraft was not being used.
I experienced this bug on a modified Bevo Tech Pack Full 7 [MC 1.7.10] installation:
Additonals mods installed: Mariculture, QuiverBow, MagicCrops and [of course] BigReactors.

Which version of BigReactors is installed? This was a bug with the early X releases.

My apologies, I thought that I put that in the original post. This bug was found on 0.4.0rc3.
UPDATE: It appears that rather than converting waste into fuel, the waste and any quantities of fuel that cannot be converted into ingots are destroyed. The ejected fuel is still duped times the number of ports.

Ah, I expect I know what this is. It's a leftover from when I rewrote the internals of the reactor's fueling mechanism. I'll get this fixed.