There is no such thing as a stupid question (my teachers would always say) unless it's that one...
haha, just messing... My metalcore projects are almost exclusively in drop B so i've had this very same problem. It's a combination of things, many of what people have said here already ring true but there's more that can be said.
+1 on the use of vst or plugin tuners. They suck donkey dick, I downloaded a strobe tuner on my iphone for like $2.99 and it works wonders believe it or not.
+1 on the use of thicker gauge strings, in my experiences even the Ernie balls 12-56 "Not Even Slinky's" is on the thin side for drop B tuning. I have a 60 on my E string cause alot of times I like to go down into A# for practice or to write and don't want to change out the strings everytime but it's more fitted for B, but it seems you already have 60 so that shouldn't really be an issue.
+1 on the 12th harmonic BUT here's the deal... you really should intonate your guitar for that to work right. It's not hard to do, you can learn how by watching some videos on youtube, but your guitar should always be intonated anyhow, the cheaper the guitar the more often it will go out, which brings me to the next topic... DON'T RECORD WITH CHEAP GUITARS!!
I can't stress that last part enough. I can't tell you how many times some kids roll into my studio space wanting to do a single, pay the basic rate and decide to stick with their gear. Every damn time, I say "before you come in take your guitars to have a fresh setup and intonation if you want this to sound as best as possible." Sure as the sun sets in the west towards the end of the tracking session their notes are going a few cents flat and it fucks up THE WHOLE THING, becuase they didn't want to spend a few extra dollars to have it setup properly. Guess what, that solo at the end, sounds like the irritable brakes on the POS volkswagen they rolled in on. Oh shit, we need to redo a lead in the beginning!? Guess what! Now the ENTIRE SONG sounds like shit. Sorry kids, nothing I can really do about that! But atleast your triggered drums and vocals will sound beast
. Ha Ha! So yea, at first try a hardware tuner, if not that the strings, still no dice? Your guitar sucks. Get a new guitar. SirKnuckles Out.