Please help I've got a problem that seams unique at least to me.

My muzzle loader only fires the cap every other time.
Unfortunately I missed my buck before I figured out the timing.
It seams that if it is cocked for some time ( haven't gotten a time frame on this yet) if fails to fire the cap, when I work the bolt it will fire ( the same cap), or when I put on a new cap (working the bolt it fires fine). Does this sound like spring fatigue. Any help on where to start would be greatly appreciated.

Sounds like a Remington 700 ML. They are notorious for being fussy about the bolt being clean. Make sure you can clean the bolt well. This is very common problem, especially if you use tight caps like RWS or CCI Mag. The Hot Shot nipple for this gun is a little smaller in diameter, or you can simply use a small file to make sure there are no burrs or flattening of your original nipple. NEVER dry fire a muzzleloader onto a bare nipple, as it will damage it.

When you first load it do you fire a few caps to clear out the nipple and breech plug if not oil in the breech or nipple can cause it to not fire. I run a cleaning rod with patched jag down the barrel and fire off at least 3 caps and then load the charge. The same method if you are using 209 primers. I shoot a Knight inline a TC Encore using 209 primers and a Lyman Great Plaines rifle with percussion caps. And have no problems with this method.

If you are having problems with your bolt you might need to get in touch with the manufacture for service.

Good Luck

Those were both good answers. Also you may want to try chucking your nipple up in a drill and using emory cloth to polish it. If the cap isnt seating far enough the first attempt is simply pushing it all the way down. It can be hard to do that by hand if its too tight a fit.. If it was a weak spring I doubt it would fire at all. What type of "cap" are you using? To me "cap " means a # 11 or a musket cap and they need to fit well on the nipples. If its a 209 primer maybe you could clean the bolt really well. They can easily get gunked up and it doesnt take much to slow down the firing pin . Good luck