Congratulations. You've found that annoying difference in a light-duty transmission and a medium-duty transmission. The larger gears (both in diameter and mass) mean the synchro's job is MUCH harder, and it takes a finite amount of time and friction to spin up/slow down those big gears. There are ways around it though-and it will "wear in" and get better with time.

Basically the friction surfaces on the synchronizer cones doesn't have enough contact area with the friction surfaces on the gears themselves. These two friction surfaces are essentially a wet clutch-and just like clutches, they need time to "mate" together.

The situation is worsened by loose tolerances on the synchro stack-most shops do not measure the synchronizer engagement distance to make sure the friction cones are properly mating up prior to the selector collar engaging the gear. They just rely on the parts suppliers to send them synchro rings that are "close enough" and normally they're a little too small-so they take a long time to "wear in" but they are rarely oversize enough to allow a newly rebuilt transmission to grind going into gear.

10-15 thousand miles and an oil change at the 7500 mile mark will help considerably. I see this in NV3500's, NV4500's, T56's and TKO's in Ford/Chevy/Mopar, FS5R30A and FS5R60A transmissions in Nissans, and some of the older heavy-duty Ford transmissions.