This has been the case for as long as I can remember, it's not new in the beta patches 
But yes, it is annoying when you have to wait for the bonuses to kick in.
I think the issue is with this:
numEntryVehicles
Level:0 5.000000
Level:1 6.000000
Level:2 7.000000
travelTime 30.000000 <<--- culprit
Basically the way it works is each capital's colonize ability calls a generic buff:
buffInstantActionType "ColonizePlanet"
And then to add the race-specific buffs this gets called:
afterColonizeBuffType "BuffTechCapitalColonize" (replace buff file name for the races, vasari use BuffPlanetConstructionBoost)
The problem is I think the game waits for the EntryVehicles to stop their 30 second travel before it calls the afterColonize buff. There's nothing in the buffs themselves that give them a delay, so this is the only thing that makes sense.
Tonight I'm going to test out dropping the travelTime in 1.05 and see if it changes anything to confirm/deny my suspicion.
