Events that are traumatic to the body in some way like car accidents or surgery have been known to trigger RA, but only in people who have a genetic predisposition to this disease.

I have two suggestions for you. First, given that you've been on your meds for six months, they should have kicked in by now. If you still have disease activity - in addition to pain, redness and swelling in your joints - that means your disease is not well suppressed. Speak to your rheumatologist about treatment options, including increasing the dose of your current medication, adding another of the DMARDs or looking into another medication altogether, like e.g., Arava or one of the Biologics.

Second, if you RA is well suppressed, your pain may be due to something else. Your shoulder and neck could be aggravated by repetitive strain - do you spend a lot of time in e.g., your job using your hands and arms? You may also want to check out the possibility of fibromyalgia - many people who have RA have another condition on top of that and fibromyalgia can cause pain in muscles and tendons, including that burning pain you describe.  Check out Lisa Emrich's recent post on RA and fibromyalgia and you may also want to take a look at the fibromyalgia area of our Chronic Pain site for more information - if anything rings a bell, see your doctor.