Ahem, well-- a little 'guru' goes a long way; the Muzzleloading Maharishi I'm not. :roll:
In a broad sense, I've found most .45 caliber muzzleloaders to be far less forgiving and more temperamental than their .50 cal counterparts. I did have some very respectable groups with my .45 Encore barrel-- in this "one incident" example, the 275 gr. Powerbelt (pushed by 90 gr. T 7 FFG or FFFg) did well.
The possibility also exists that you just have a poor barrel-- T/C has been known to let a few barrels with variable rifling depth slip out. In my Contender G2, the .40 / 45 220 gr. Dead Centers have shot MOA with 100 gr. T 7 FFg. The 200 gr. Shockwaves have been reported on favorably as well.
So, there are no great words from the hilltop-- just make sure your Encore's forearm is fully floated away from the barrel, and try a few different combinations. I'm not sure what has been tried or what has frustrated you to this point, or what your current groups are-- but, at the point you feel you've done your due diligence to a reasonable degree it may well be time to have Thompson look at it. They do stand behind their products. :grin: