In extruder.cpp line 1110 you see
#if HAVE_HEATED_BED
writeInt(EPR_BED_PREHEAT_TEMP, Com::tEPRPreheatBedTemp);
writeByte(EPR_BED_HEAT_MANAGER, Com::tEPRBedHeatManager);
writeByte(EPR_BED_DRIVE_MAX, Com::tEPRBedPIDDriveMax);
writeByte(EPR_BED_DRIVE_MIN, Com::tEPRBedPIDDriveMin);
writeFloat(EPR_BED_PID_PGAIN, Com::tEPRBedPGain);
writeFloat(EPR_BED_PID_IGAIN, Com::tEPRBedIGain);
writeFloat(EPR_BED_PID_DGAIN, Com::tEPRBedDGain);
writeByte(EPR_BED_PID_MAX, Com::tEPRBedPISMaxValue);
#if ENABLED(TEMP_GAIN)
writeFloat(EPR_HEATED_BED_GAIN, PSTR("Bed Temp. Gain"), 4);
writeFloat(EPR_HEATED_BED_BIAS, PSTR("Bed Temp. Bias [degC]"), 4);
#endif
#endif
for 1.0.4dev firmware. There you see it writes the bed values after bed PID values. It might not detect you enabling/disabling gain so eeprom gets not initialized unless you reset eeprom with
M502
M500
Were you using 1.0.3 firmware?