#1
I finally changed the strings on my EC-1000 to .12 gauge and tuned it down to B. At first it sounded really awesome while I was chugging along for fun, but the next day I tried to play actual songs (after retuning, of course), and the open notes sound quite off somehow. I thought the problem might be intonation, but then I usually read that wrong intonation would be noticeable if you go higher on the fretboard, which is not the case here.

Is it most likely a problem with the action? Like I said, it only affects the open notes, fretted notes sound fine to me.
#2
If you haven't intonated it I'd do that anyway just in case, if not then it might be a tension thing, when my guitars are in drop G# if I hit the low G# too hard it bends out of tune then goes back in, that might be the case here? Apart from that I can't think of anything
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#3
IF you lowered the strings that much it probably needs a good setup. Lowering the pitch also reduces string tension on the neck, and can allow the neck relief to change. Action probably needs to be raised, intonation should be checked. I doubt whether intonation would change much, but it may be possible.

Your description doesn't tell me whether this is a buzzing sound, but if neck relief has changed that is a possibility. It also makes sense that it didn't show itself till the next day, a truss rod adjustment takes overnight to settle in, that's because the wood doesn't snap into place instantly when the adjustment is made. It moves gradually. Same if you reduce string tension.

With lower tuning you also have a wider vibrational pattern, so both action and truss rod may need to be adjusted to give the strings clearance in the middle of the neck. Check here

http://www.frets.com/FretsPages/pagelist.html

Look in the Instrument Setup section, good info on setups. Be careful if you need to adjust the truss rod, it's not hard to break it. Only adjust it if you need to, once you learn how to determine that.

That said, I think your neck lost a lot of its relief due to lowered string tension, truss rod needs to be loosened to give it more neck relief. 1/4 turn, let it sit overnight, check it again. The link above says .013" to .023", with low tuning you might need it on the high side. Strings vibrate in a pattern similar to a jump rope, wide in the middle, almost nothing at the ends. Lower tension they vibrate even wider in the middle, so you might need more neck relief. Since it takes the wood a while to move into place, it didn't show up till the next day.

First thing to do is determine if what you're hearing is a fret buzz though...then determine where it comes from. Then start making adjustments.
Hmmm...I wonder what this button does...
#4
Thanks for the replies, guys. Just came back from the hospital, once I'm clear again I will go through your suggestions.