Thanks, everyone for the helpful replies, much appreciated.
I am sure people with more knowledge on setups will be along, but in the meantime, could you be pushing too hard? If you push down too hard on the strings the notes go sharp. If I had known when I played as a teen how lightly you really needed to fret I likely would not have had decades away before taking it up again. If you are super experienced please ignore, if not, try fretting a note just enough to mute it then gradually push harder while picking until the note rings clear, you may be surprised how little it takes.
Best of luck with it, there will be an answer.
I thought that could be the issue too as I've only been playing for a few years now, but when testing by really softly pressing a note on the problem strings, they still go sharp so it must be something else.
Has the intonation changed from when you first bought the guitar? If so, it might be because your strings are pretty old, considering you haven’t changed them since you bought the guitar six months ago. Before doing anything drastic or costly, I’d start by putting on a new set of strings. I'm not absolutely positive that'll solve the problem, but a string change often cures a lot of ills.
Now, this I'm not quite sure about, it wasn't something I noticed before, but I don't know if my ear has somehow gained this ability and therefore I'm only just noticing it now or if it's only just become an issue (probably the latter). I've got an extra set of the same strings that are on it now (EJ16's), or should I get Elixr's?
Got to be honest, I'm not a fan of new strings so I was putting off changing them because these had settled in, new strings are just too bright for me but I'll definitely get them changed, just want to order some ebony bridge pins first!
I'll post an update once I've changed the strings.
Hey Luke,
Not a long post at all. Welcome aboard, and congrats on a great guitar!!
I presume you are using a decent electronic tuner to verify the fretted notes going sharp, correct? If so, what you need is the saddle reshaped to adjust for intonation. Taylor is very good at establishing good intonation, but perhaps this one slipped by QC. If you bought this guitar new, call the factory and they will give you the names of Authorized Taylor techs in your area who can address your intonation under warranty for free. If you did not buy the guitar new, then the same job will cost you a nominal fee (not expensive but ultimately depends on region) from said tech. Btw, Dennis is right about old strings vs new: strings with lots of play will absolutely alter intonation. Hope that helps you a bit. 
Edward
Thanks a lot! Apart from the intonation issue and wishing it had a bit more low-end (the bass sound a bit weak depending on which room in the house I play in), I've been really enjoying it, Taylor sure does know how to make a great guitar.
Yes, I'm using the NS Micro Soundhole tuner, and it confirms the notes are going sharp. It is second-hand so no warranty, but there is a Taylor Authorised tech at a guitar shop in my city, I'm gonna send them an email, to get info on the services and prices since they don't list those on their website and if a string change doesn't solve the issue I'll have no choice but to take it into them for a set-up.
The strange thing is I've played guitars with years-old strings on them with absolutely no intonation issues so I find it odd that these lasted only a few months, maybe they were duds, or maybe D'Addario's just aren't as long-lasting as Elixr's or Martins, but I'll definitely change them, it's certainly an easy and cheap thing to do before getting a set-up.
Lots of good replies so far. Old strings are the most likely culprit, IMHO. One of the ways to tell that strings are shot is if they won't get into or stay in tune. Another possibility is that the compensated saddle somehow got flipped during a string change. The unwound b string (second string) should have a distinct step to help that string, and the saddle must be positioned so that the length of the b string is longer than its neighbors.
It is the nature of the acoustic guitar beast that wound strings tend to go sharper when fretted or capo'ed. For me, the tuning *always* needs to be tweaked when using a capo, regardless of brand -- and I've tried them all. Shubb Classic is my #1 followed by the Dunlop Trigger at #2. The one that is by far the worst for me is the Kyser because the spring is so strong that it bends strings way out of tune. Hope this helps.
I've checked the saddle and it looks to be in the correct position, I can post a pic if that'd help!
The funny thing is I am using a Kyser, it's a great capo but as you say the spring is far too strong, it not only affects intonation but also the tone, definitely part of the issue I'm having but not sure if it's the main culprit. Guess I'll be asking Santa for a Shubb this Christmas though