Unfortunately, on a 2-core machine the packaging process cannot go wide 
You may want to edit BaseEngine.ini and set
[DevOptions.Shaders]
bAllowCompilingThroughWorkers=false
Since in your case spawning separate shader compile workers probably only makes the situation worse. The discrepancy between the times is perhaps because on second (and later) packaging you’re already using the cached data from Engine/DerivedDataCache.
I recommend finding a quad-core or better machine for packaging (the more cores, the better).