Go through and tighten up all the bolts..you should do this anyways as the heat and expansion from the exhaust can loosen things up..put a wrench on all the bolts..
The JBAs have been know to blow out the packing..usually after some time..I heard they redesigned the muffler recently...so who knows..
Go underneath the truck and tap on the muffler with a wrench or something, if you hear rattling or like rice, its probably shot..
Just changed mine out for a borla. Once I put catless bpipes I could hear the same thing, on start up but would go away and at certain rpm would do it. I took the rubber handle of a hammer and taped on the muffler and it was 100% from the muffler internally. Of course it was 5 years old so not to bad...
If it happens when its cold and goes away when its hot, it means a weld inside the muffler is broken. The pieces rattle when its cold but when it warms up the piece expands and pushed against the piece it rattles against. Causing the rattle to go away.
As recommended before, go through and make sure the hangers arent touching anything and that all the clamps are nice and tight. If the problem persists, call JBA and get a new muffler.
Call Pertronix directly,recorded message will give you a tech.support number.Call this no. and tell them your issue.You will have to fax or e-mail them your invoice with purchase date