As of 31 March 2013, England's* Primary Care Trusts (PCTs), who used to pay for treatment for Gender Dysphoria, have been abolished. The old PCTs have been replaced by Clinical Commissioning Groups (CCGs) - but CCGs are not responsible for paying for treatment for GD. GD treatment is now funded by NHS England's Local Area Teams (LATs), who are entirely different organisations to the old PCTs.
This means that if you have a funding application or appeal that hasn't yet been approved, there is a possibility that your application might be delayed. If it was sent to your old PCT (now your CCG) they might simply reject it because they don't deal with GD funding any more. You might then face a wait whilst a new application is made to the new LAT instead.
New patients shouldn't notice any difference. You still have to go to your GP as the first port of call and they should commission the services you need accordingly - they'll just send your application to your LAT. However, it remains to be seen whether we will face delays in our treatment whilst everyone gets used to the new system - particularly if your doctor doesn't deal with a lot of trans* patients.
In theory, all doctors and GICs should be aware of this and recent applications should've been sent to your new LAT. Also, you'd hope that your old PCT would've handed over their pending applications to your new LAT when they closed down. But it's possible that they didn't and your referring doctor won't even realise that the system
has changed until they get the refusal letter from your old PCT. You'd then have to wait even longer whilst they make a new application to your LAT... all of which adds up to an additional delay that I doubt anyone here needs in their lives.
As a precaution, I would suggest that anyone who is concerned about an outstanding funding application or appeal should contact whoever has made the application (i.e. your GIC; your doctor; your psychiatrist) and ask them to check whether it is being processed by the right people.
And if you're a new patient, it might not hurt to mention in passing that you've heard that it's the LAT that funds GD treatment now. Just in case your doctor doesn't realise it yet.

Here's a guide from NHS England about how and why they will fund specialist treatment, and why the new CCGs will not fund it. The provision for GD treatment for under-18s is on page 126; the provision for adults is on page 128:
http://www.england.nhs.uk/wp-content/uploads/2012/12/pss-manual.pdfAnd as a caveat, I don't work for the NHS - I just wanted to share the information I've researched whilst attempting to figure out how exceptional funding is decided now that our PCTs have been abolished.
* Sorry, but I haven't researched whether the rules have changed in Scotland, Wales or Northern Ireland.