#1
Just bought a set of strings(7 string guitar), went up to a slightly thicker gauge. old strings were 10-54 , went up to 10-60, the strings sit in the nut fine. But they don't seem to intonate. Well the E and A sound off when played together., the low b is fine.

Maybe the strings are too thick for the nut? I don't think it's the problem but it's possible. or maybe an old set of strings?

The strings I bought weren't sealed, just in little paper sleeves. I intonated the low E and A but even though they're intotanted when I play them together it sounds flat. I think it's from the A string.

Possible bad string?
#2
I guess a bad string is possible but:

1. Did you reset the neck relief, or at least measure it?
2. Did the action change by putting on the new guage of strings? At the first fret? At the 12th? At the 21st?
3. What tuner did you use to set intonation?
Guitars:
Jackson Kelly KE3 - MIJ (Distortion/Jazz)
Jackson DKMGT Dinky (EMG 81/85)
ESP E-II Eclipse Custom (JB/'59)
ESP LTD EC-1001FR (EMG 81/60)
Fender MIM Strat

Amps:
Mesa/Boogie Dual Rectifier Roadster 212
Laney IronHeart IRT-Studio
Peavey Vypyr 30
Peavey ReValver Amp Sims
TOOOO many T.C. Electronic Pedals. . .