NetSuite Saved Search where {location} = {user.location}?

In a lot of case, when you use Numeric Formula, it seems like NS prefer using internalIds, so use this in your formula and it should work (tested):

CASE WHEN {location.id} = {user.location.id} THEN 1 ELSE 0 END

Most likely due to NetSuite perceiving the possibility of data type differences. Try wrapping your location fields in NVL and/or TO_CHAR or using ...location.id}