Raymond,
I'm using the late 2012 i7 iMac 27" with a 3 TB Fusion. You are not going crazy. What's happened to you is what happened to me. I tried to do Bootcamp Assistant for the first time, and it froze on the partitioning phase. I literally let the software run for 20 hours trying to wait it out, just to be on the safe side. Eventually, I quit the task, and that's when I noticed the issue with two logical partitions. I had a separate 800.2 gb partition that I could not re-merge with the first partition, no matter what. No option was available in Disk Utility that would work. As Greglawnjee suggests above, repairing the top-level Macintosh HD did nothing. Rebooting with CMD-R and repeating this process did nothing, either.
Then, I tried what another user suggested which was to reboot into the Windows install and manually delete the offending partition (it's hard to decide which, as the sizes in Windows vary from what is reported in OSX, and I wish someone would screenshot what to keep and what to delete). Anyway, after this, I knew that I'd have a messed-up Mac install that I'd have to recover from Time Machine.
At this point, OS X had to do an internet recovery in order to get working again. OS X correctly stated that I had a 3.12 TB partition in Disk Utility. I ran Bootcamp Assistant and let it do its magic. I chose a 520 gb partition (same annoying slider issue as someone else mentioned, I really wanted to put in 512 gb but the slider would not land on that size).
At this point, after installing Windows 8 and doing a Time Machine recovery from the CMD-R screen, I ran Disk Utility and had 3 partitions, the original Macintosh HD partition, a Bootcamp partition, and another Macintosh HD partition. However, the difference this time is that my Finder window reports one logical Mac partition of about 2.5 TB, so OSX is doing some kind of magic behind the scenes to link those two disparate partitions together.
This does bother me, and I do wish that Apple would correct the Bootcamp Assistant to resolve the hang issue and to help users recover from these fragmented partitions when this does occur.
Still, my best bet is to reiterate what someone else already said, and that is to use your Windows installer to remove that annoying partition which OSX is seemingly incapable of removing itself. Then, when you do your system restore from Time Machine, it will logically read as 3 TB only to be split in half physically by the Bootcamp partition.
I hope some of this makes sense. I'm sort of confusing myself here the more I read what happened to me.