For a few months, a select group of NJ Transit commuters shared a secret edge over their rush-hour rivals: early insight into unpredictable track assignments at Penn Station.

But that crucial advantage evaporated last week when the railroad blocked a data feed used to decode track assignments. Clever Commute, a start-up website, had begun selling a premium train information site for $3.99 per month that include the track listings—without NJ Transit's blessing.

A...