Jeremy,
What grade alcohol are you using? Rubbing alcohol is 50% water. I use 91% isopropyl as a good cleaning alcohol. Stove alcohol or solvent alcohol from the hardware store is good, also.
I don't actually pour alcohol down the bore, gust a good damp patch. Though I do usually leave the nipple out for a couple days after cleaning the rifle to let everything evaporate out. After I clean I wipe with Birchwood Casey Sheath and then, before shooting again, I wipe with alcohol and then a dry patch.
Any time you leave a percussion gun sit a week or more it's not a bad idea to dribble in a few kernels of powder (don't plug the channel, just a few). As an experiment I left my New Englander loaded 11 months. Fired first pull without doing anything put capping and pulling the trigger. (CCI regular #11 cap).
Any residual oil or lube from the patch can leach into a charge and "kill" it. I had a vegetable fiber wad between the patch and the powder in that instance; which I usually add for hunting as I do tend to leave them loaded between hunts.