You have an IGH hub with vertical dropout. Do you use a chain tensioner, or did the chain just work out right? If no tensioner, is there some slack in the lower loop?
Also do you have the right keyed anti-rotation washers, and do they key to the dropouts properly, with everything aligned?
How and why is the wheel not aligning right, is the axle width wrong, or is something in the way?
If everything external is right, and given that you've opened the hub once already, I'd open it again and see if there's anything obvious such as migrated grease making the pawls sticky, dirt where you don't want it, or any chipped parts or metal chips in the oil sump.
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