From what I can see the only changes to the 3.0L was in 1991 when they changed the pistons and made a few minor engine block changes and then back in 1998 when they changed the intake and cam to up the power to 155 HP.
I would also make sure that the Consumer Reports article was definitely looking only at the 3.0L Vulcan engine and not the newer Duratec 3.0, which has had some issues.
I have read a few articles over the last few years that didn't seem to realize that these were very different engines and not one in the same. The only 3.0L engine that is used in the Ranger is the Vulcan which is assembled at the Lima Engine plant and has had an excellent durability record.
Such a rating may also be due to simply selling more 3.0L enignes those years.
In 2001 Ford began a huge push to market the Ranger to a younger group of buyers as well, many of those who probably tend to be harder on their trucks than the traditional older buyer. The Ranger Edge was created for this market as well, mostly geared toward 18 to 30 year olds. The 3.0L was the standard engine for the Ranger Edge.
(Not that everyone abuses their truck but there's also probably fewer senior citizens that baja their Rangers than do many 18 to 30 years old owners).