At the beginning of WWII the railroads coming out of the great depression and had vast excess capacity and plenty of available labor to ramp up for WWII.

During WWI, the US economy was already booming with war trade to France and Britain, RR's were at or near capacity, still operating with a lot of obsolete equipment, especially on the eastern roads, which had resulted in a national level UP style meltdown.

The WWI "takeover" allowed the government to better prioritize capital investments in new equipment (e.g. USRA locos), to better prioritize the routes and traffic, and to use the available capacity more efficiently, is the probably the simple answer...