Looking at Google Earth, the yard is just to the east of Gladstone. Put-ins from that yard have to move a short distance west to Gladstone, then change ends and do their run to Hoboken. The station can only accommodate one train, and they have to wait till the previous train has cleared the yard before moving the next train in. It's not like most of the other yards in the system where the train can go directly into the station from the yard and then complete their runs without changing ends. Since 6406 is a Midtown Direct, it runs a longer train and has higher ridership than the regular Hoboken trains. That means that it needs more time to load up and change ends, and more difficult to have it depart on time. For that reason, they likely decided that it was easier to run 6406 directly to Peapack to begin it's run, since it's only 12 minutes behind Hoboken train 404. Passengers from Gladstone wanting to ride the Midtown Direct can transfer at Peapack.