Well, we paid for a preferred room, back then the travel agent we dealt with (who was great) had specifically told them we desired a king room and it was our honeymoon... at no time was she or us told of "extra charges" beyond "preferred", and that that we had nothing to worry about...
until we were there to check in and apparently it was much to late then.
If you use a travel agent in the future to book WDW trips, use a different one than you used the last time. Either she didn't know enough about WDW, or she didn't communicate well with you, or she didn't understand/anticipate your wants and needs ... whichever, I wouldn't use that travel agent a second time. To me, the most important attribute of a good travel agent is excruciating attention to detail. Sadly, if your TA didn't know there were upcharges and specific reservations involved, then she should not have booked the trip at all.
Please allow me to explain how it works at CBR, in case it will help you (or someone else) in the future ....
Over and above a standard room, there are 3 possible upgrades that you can reserve and pay for.
PREFERRED LOCATION: a room in one of the 6 buildlings closest to Old Port Royale, the complex that has the food court, main pool, shops, etc. There is nothing about a preferred location room that makes it any better than any other room except its proximity to OPR.
WATER VIEW: a room with a view of Barefoot Bay (the lake) or your village's quiet pool. Each village has some water view rooms, as each village has some lake frontage and each village has its own quiet pool. There's no way to guarantee whether the view will be of the lake or of a pool that is typically anything but quiet.
KING-SIZE BED: self-explanatory.
Each of the above categories must be reserved and paid for in order to be guaranteed. If it is not paid for, then it will be put in simply as a request, and of course requests can't be guaranteed.
Each of the above categories carries a per-night upcharge, which ranges between $15-$26 extra per night, depending on the season.
[In your post you used the term "preferred room." That's not a term that CBR uses. It's ambiguous, and might lead you to believe that it's a special room with all sorts of special amenities. No such thing at CBR.]
Now here's the weird thing: Disney will not permit you to reserve and pay for more than one of these categories. It amazes me that Disney won't take more of our money, but the fact is that they won't.
In other words, you can pay $15 extra per night for a water view room, OR you can pay $15 extra per night for a king-size bed in your room, BUT, you can't pay $30 extra per night for a water view room with a king-size bed. Strange but true ....
So in your case, if your travel agent thought she guaranteed you a king-size bed in a preferred location room, she was sadly mistaken, as you now know.
If you want both, Disney forces you to make a decision. Which do you want more??? Whichever upgrade you want more, reserve and pay for that one, and then request the other one.
Now, there ARE rooms that happen to have more than one of those upgrades. For example, since every village has some water view rooms, that means that some of the preferred location rooms are also water view rooms. Getting a room with more than one upgrade is simply a matter of luck.
If you go back to WDW, please do your own homework, and then even if you use a TA you'll be able to know exactly what you want. I do this no matter where I travel ... for me, doing the research before the trip is half the fun.
GOOD LUCK!