I have had my Mk2a for about a year now, maybe a bit longer. Recently I got the great idea to upgrade to 2.0 of the consumer software and the lastest hijak kernal. Now when adjusting my EQ the band will not drop below 50 wtf? I am driving 2 10" Kicker Comp VR in a custom box tuned to 30 and i usually increase that 1-2 db before it hits the alpine mdr-m500 amps. Is there a way to force this thing to go below 50 or do i just need to set the Q to a low setting to bring the other frequencies up?

You need to adjust the Q setting, that is correct.

The problem with setting frequencies below 50 was that you could possibly create certain value combinations that would make the DSP produce low frequency static, which potentially might damage your speakers.

Downgrade to 2.0-beta13.
Set EQ to taste (avoiding the insanely high Q settings that were required to cause the noise problem). Save EQ setting.
Upgrade back to 2.0-final.
Your EQ setting will be intact w/sub 50Hz band. Just don't try to change it!
Enjoy.

Has this been changed in 3.0a? Or am I going to be stuck with 2.0-final if I want my system to sound right? I'm too chicken to try 3.0 on my one & only Empeg to find out.

Remember that 2.0 was the fixed version. The fact that it won't let you set it below 50 is the intended behavior. So as they go forward in versions, it's likely that they'll continue to have it be the same behavior.

Actually, a fixed version would still allow sub 50Hz EQ, but not allow you to choose the extreme combinations of Q & levels that would "break" the DSP.
I probably wouldn't be so ticked off about this if my truck didn't require a fairly deep "cut" at 32Hz to smooth out the bass (as measured with a Sencore 12th octave RTA).

but not allow you to choose the extreme combinations of Q & levels that would "break" the DSP

Therein lies the problem. That wasn't possible. The DSP-breaking combinations required extremely strange and specific settings which fell in the middle of other acceptable ranges. The only solutions are: Allow people to break the DSP, or prevent them from breaking the DSP by brute force. They chose the latter.