there is no need to waste money popping caps in an empty chamber to ensure a clear nipple.
A needle or paper clip in the hole is fine to verify clear. or look for daylight.
Very possible you have oil contamination in that chamber,
the hard way is pull the ball dump and clean
Easier way, pull the nipple, verify it is clean and same height as the others.
Use the needle or paper clip to gently scrape some powder loose and out.
Trickle fresh powder into the hole. replace the nipple, put cylinder back in gun.
Cap and fire.
Next time before shooting. (if you have not been doing it already) thoroughly clean each chamber with a swab of rubbing alcohol ( personally after cleaning I don't lube the chambers, but then again I reload immediately).
Don't use crisco as a lube and don't use a petroleum based lube in the chambers or bores.
Personally don't know why you are using filler either. Load the gun with 25 to 30 gr and you shouldn't need to worry about seated ball height.
As others have said. Pyrodex is a bit harder to ignite than real BP, but that doesn't explain just one dead cylinder.
I've used Pyrodex P off and on for years never a ignition problem, same with real BP and T7.
I've left mine loaded as long as two year, and never failed to go bang with any powder. Except the occasional dud cap now and then.