No dude its because its out of tune or youre playing the chord wrong. Also don't mix new strings and old strings. Don't mix strings from different gauge sets unless you know the sound youre going for, or you know what youre doing. The D string isn't one I'd switch out anyway. The old strings are also very likely not intonated correctly anymore. You should get a fresh set of strings and restring the whole thing starting from the bottom, doing one at a time. Get it all tuned a little flat, and then tune it all up and stretch them out until they set. Also, you should know that new strings, especially light gauge strings, will not hold their tuning until thoroughly worked and stretched out. Depending on how well you string it, it could take longer than normal.
Taking intonation into account.... if youre playing a power chord up the neck... it's gonna sound like SHIT with bad intonation, and it will be very recognizably shitty. Power chords are 2 different notes at perfect intervals, which really sing the tune of bad tuning. In fact, when i tune by ear., ill use perfect fifths to fine tune some shit if i cant hear it, rather than octaves or unisions. Up the neck, bad intonation will result in a correctly tuned open string being out of tune when fretted (the higher up the neck, the more out of tune).
If you are just now getting into guitars, intonating your first guitar is probably not a smart idea. If you have changed string gauges, you will probably have to adjust the action on the guitar, which will throw the intonation out further. If you have not changed string gauges, then the intonation is likely off because of the old strings, so restringing should solve the issue.
I tend to like heavier top strings GBe compared to the normal sizes you'd find in like a pack of .056 - .012 (12's) so id do like .50 - .12..... somethin like that. Better sustain and body on the higher strings, which tend to be twangy IMO, especially because i play with my fingers, and the thumb tends to hit the bottom strings, giving them a much fuller sound (much to my dismay).
For an acoustic... IDK what to tell you for a first guitar. Don't get a yamaha or an alvarez, they play like shit. Not cost effective. Public schools buy them, that's how bad they are. For an electric, check out Ibanez. I'm assuming you want to play like pop/rock/metal kinda stuff, and ibanez solids are cheap, play well, and sound good enough to pull that shit off. Ibanez also makes some great models (their higher end stock includes some awesome artist and sig models). Epiphone makes some ok shit as well. Their highest end stuff, I have never been to fond of, whether it's great or not. I just got done playing a Jay Turser as my routine guitar (and gig guitar actually). It was 200 bucks and i liked it more than the 2000 dollar PRS CE 24 Custom i got years before that. Jay Turser makes great, cheap copies of some nice, big name models. I would look at their PRS models and their Gibson models.
DO NOT go out and blow money on a Les Paul just because that's the guitar everyone plays. Wait til you're sure you got the $ and you're going to spend some time in the practice room. Wait til you've played a lot of different models, at least at guitar center or some shit, as well. Despite what many will tell you, it is NOT the silver bullet guitar. It's great, but that doesn't mean it's great for you. All of this goes for nice Strat models as well.
In terms of what strings to buy, just go D'Addario. Never had problems with them, they got shit tons of different sets, and they are reasonably priced. Get normal, hex wound sets. Flatwounds and roundwounds will die NOTICEABLY faster. If you want your strings to last longer, keep a cloth in your case and use it to wipe down the neck whenever your done playing/practicing.
For a TUNER get this thing called a "Snark." They recently came out I believe (within the last year). They clip on to the headstock and tune based on vibrations. It's got a metro in it, too. I don't think they're too expensive, and they are certainly accurate and easy to tune with. If you plan on gigging, you can use it to tune while everyone else in the band is blowing between songs (as it doesn't use a classic mic to tune).
For an AMP you really have to go out and play a whole lot of them. There are a handful of very famous series that include a fuck ton of different models with different power, speakers, EQ's, gadgets, and PRICES. If you aren't gigging for a whlie, get a small practice amp (not too small). Peavey makes some nice little models, but they tend to be overdone with effects and other bullshit. In my opinion, if you want effects, don't get an amp that has effects, get a really nice sounding amp and then get pedals. Otherwise, you'll end up getting this amp that has sacrificed some sound quality for shit tons of col gadgets, and you'll only end up using about half (at most) of those gadgets. Fender makes fantastic amps that can be used in a wide variety of situations. They are expensive, though.
CABLES idgaf what people say, monster cables are worth it. All the other cables iv'e had have just died on me. Monster cables are way more expensive, but will not break, and the warranty is fantastic. You also won't have to worry about sound quality.
Hope this helps.