I'm an electrical hack, but have may be able to jog some ideas...
First thing I'd do is disconnect the 2nd battery, charge it, then see if it's still charged after a day or 2. Just to rule out that it's just a bad battery. Or possibly point you to something going awry with your dual setup- do you have a boxed system (IBS, Hellroaring, Nat Luna, etc) or homebrew setup?
Another test is pull all your fuses out of the Blue Sea box, then measure voltage at the battery and at the box. See if there's a voltage drop? If there is, then something's funky in the line between the battery and the box. If not, then one at a time put fuses back and measure what changes. Or leave the fuses out and see if your good battery stays good... eventually you'll isolate the drain. hth!
82 fj40, 99 uzj100, 06 gx470
97 DR650, 05 525EXC, 01 XT225, 89 TW200, 09 TTR125, 07 TTR90, 07 CRF50