This is undoubtedly what happened. 3500 miles is a lot for one chain. Once the chain is stretched past 1/16" per 12 links, the rate of cog wear accelerates rapidly. Putting a new chain on a worn cog produces the effect described by the OP. If the cogs is only worn a little, things will smooth out as the new chain wears slightly. If the wear is more severe, its time to replace the cog, and possibly the chainring.