There may be something to this, PixieCamper.
I was at the Fort in mid-April of this year and went on a bike ride several times a day in the various loops. It's been my sense that in the spring when weather is so comfortable that the Fort gets a lot of weekend campers coming in from the area around Orlando (a couple hour circle) on Friday and leaving out on Sunday. That's what I expected this year during my visit.
What I saw (and related in my Trip Report) was how strange it was the way the Fort filled up over the weekend I was there. Sure the Partial/Tent sites were full both in loops 1500 and 2000. Tenters, Cub Scouts, weekend folks, etc. But the next most affordable type of sites, the Full (loops 1600-1900) had the two loops in back that each had ONE camper in them the entire weekend (1800 and 1900). All the weekend folks were assigned into 1600 and 1900.
So to me that indicates two things. First, PixieCamper's point is probably true. The travel agencies in question might be leaving the Tent/Partial sites to us regular folk since there are only two loops of that type. But they might be going after the next lowest rung of the ladder which is the Full loops. Maybe that's what was happening on my visit in April like it was happening to Pixie's visit in May.
But that leads me to my second point - I think this is being done with the full knowledge of the Fort management (or they are at least looking the other way). They probably think that there are PLENTY of sites for Full/Preferred/Premium and if folks can't get a Full they'll opt to upgrade their site type. So reallly they might feel they are making room money on sites that would otherwise be empty and non-revenue producing. So it's gravy to them.
But the practice may have grown to the point where it's starting to crowd out folks like the OP amylevan that want to come and don't have a site to upgrade to. And they won't buy at the TP, eat at TE, pay for the recreation (Segway, boat rental), or drop bling for an expensive Disney golf cart (ok,
THAT might get their attention

). Then it will have a detrimental effect on the bottom line. If on-site benefits (free parking, extra hours) are available to off-site guests, it dilutes the value of staying on-site and paying a premium for a room. Once the genie is out of the bottle here, it's hard to limit or contain it.
So this practice may explain why I saw two nearly empty loops. I would think if this was NOT happening, Disney would try to evenly assign the Full loops to share/spread the wear-and-tear on the infrastructure and capital assets (such as they are). The fact that all four Full loops weren't more-or-less equally assigned leads me to believe the Management is a willing participant.
Bama Ed
PS - I also believe that someone on the payroll for Disney reviews Disney fan forums and web sites such as this one.