When Doc sets the timer for the trip, he enters 52,594,560 seconds. This is only 608 days, or about 1 year 8 months, not the 100 years he was planning to travel. It is very unlikely someone of his background would make such a mistake.
The 52+million seconds mentioned is the number of MINUTES in 100 years, not the number of SECONDS. Oops, someone did bad math.