What brand did you replace them with?
I had a similar symptoms after replacing mine. Went away after a couple of hundred miles.
Have you greased the new ball joints?
I replaced them with synergy's
Would you say it seems like it won't automatically center after a slight turn or lane change? I've had king pins on heavy trucks do this when they are set up too tight, it is scary if bad enough. If you jack up the front does it seem like it is very difficult to turn the wheel? If the cause is tight ball joints it may loosen up after a while.
When i welded on my c gussetts and lca skids i replaced my ball joints after. Ever since then the steering is horrible. Ive checked the alignment a few times and its in spec. The jeep constantly wants to turn right or left. Anyone have this issue before?