There is carbon, and there is carbon
However, generally speaking, carbon is a pretty good screening material which will significantly reduce the strength of any 2.4GHz signal that manages to pass through it. Fortunately, most models aren't made of 100% carbon.
The general rule is that you should keep your 2.4GHz antenna(s) at least two inches away from carbon or other conductive materials inside your model and, if the model's fuselage is made from carbon composite, route the antenna(s) so that they are outside and clear of the model. This may mean having them poking directly out like cat's whiskers, *NOT* taped down against the outside of the carbon.
When you're talking about carbon reinforcements (as opposed to wholely carbon construction) then things get a bit murkier. When carbon roving (strips) are placed closer than 5 inches (125mm) apart then they can also effectively act like a solid sheet of carbon (google "Faraday Shield") so even some strips of carbon strategically placed inside the fuselage to provide stiffness can have a negative effect on the range of 2.4GHz equipment.
However, there's often a bit of a void between theory and practice.
My experiments have shown that some 2.4GHz systems will provide perfectly adequate range despite the fact that (in theory) they shouldn't work in a hi-carbon environment.
The best/easiest way to perform a practical check these days is to use an RC system that offers telemetry information which includes the received signal strength. By monitoring the signal strength as you fly it will become very obvious if there are any issues relating to the presence of carbon in the model. Of course a 360 degree range-test in power-down mode will also provide valuable information that may show any major shortcomings in your installation.
There shouldn't be any difference between the JR and the Futaba systems as far as range goes when carbon is about -- I suspect the reasons for your observation may be to do with the precise placement of the receiver antenna(s). Sometimes, when working in a highly reflective/absorbent RF environment, repositioning the receiver antenna by just a few mm can have an astonishing effect on range.
RCModelReviews.com, just the facts.