Hey 87mark7slc, there could be a misalignment and you are wise to check for that. But if you're running new chains on old sprockets make a note of this.
#50 chain is 5/8" pitch (measured pin to pin). 5/8" = .625" As a chain and sprocket set wears out, the metal does not stretch, the chain stretches by the fact that the pins and holes ovalize. Consequently a #50 chain of 5/8" pitch (.625") becomes something like .650" pitch with the extra pin slop. What this does is wear the sprocket out to be a .650" pitch sprocket. The chain climbs higher on the teeth, and creates its own cradle for the chain roller, at a slightly larger diameter.
I made this image from a pic showing what happens when an old stretched chain is run on a new sprocket. This is the opposite of the discussion (new chain on worn sprocket) but it's the best I could come up with but it illustrates the problem of running mis-matched parts (old and new) together. Hope this makes sense. Wish I knew photoshop better. Also .650" is a gross exaggeration, probably more like .630".
Then when you put a new .625" chain on the old .650" sprocket, the chain tension cannot spread across several teeth on the sprocket, consequently ALL of the chain load goes into the ONE link, on the first tooth if driving sprocket (or last tooth of the driven sprocket). Because it's not spreading across several links, and ALL load going into one link at a time, the chain wear is very very high.
If you run new chains on "OK" sprockets, the chain will wear out (stretch) quickly to match the "OK" worn sprockets. If the sprocket is a little worn, it will settle out "OK". If the sprockets are a lot worn, you will ruin your new chain. There is a balance where replacing one or two components works OK, but if either is worn beyond a certain point you have to replace all sprockets and chain too.
Sorry I can't tell you where that sweet spot is, it depends a lot on the cost of the chains and sprockets. OI can try to find an image to help if anybody's interested. Many folks find that simply replacing all (chain & sprocket as a matched set) is better for them. Certainly it's better for "the shop" and can be better for the customer too.