Okay time to ask something rather fundamental. When you update your Client, and your Server, do you download from the FTB mod packs for both?
If you only DL the client, and drag/drop, copy/paste into your server, you're going to get duplicate mods. (Also you can end up with other conflicts like ID's, config issues, etc.)
If you're DLing both, but still ending up with Dup. issues, then I'm willing to bet it's one or more of the mods in the Folders, inside your ,mod folder. (Like I'd said above.) Most commonly this is the mod/1.6.4 folder which has the CodeChickenLib, ForgeMultiPart, and WorldCore - universal's in it. From what I've experienced, it's usually one of these 3 that gets a dup., or update.
Also I see you're using Bukkit. I use to, but won't anymore. Too much headache, and hassle to set up. That being said, Bukkit can create it's own conflicts that mess up game generation. Just in case, I'd look into JadedCat's post
Here on using MCPC, or similar. In case there's something I didn't spot. And, finally, from what I've read so far (being out of the loop on Bukkit or MCPC variants.) 1.0.11 versions of several mods aren't ready to be reconfigured by 'outside launchers' like Bukkit. Again see Jaded's post for more details.
Personally, what I do, normally, to update my versions, is I download the Server.rar from FTB launcher into a brand new folder. Extract it to the same location (usually on my Desktop for ease of use.) and then I go through the mods and double check which ones are there compared to previous versions.
Run it once until the 'world' folder is created, then kill it. (This gets all the required folders there, no guess work.)
Next I copy any core config files, or parts of files, over to that new server folder's config folder. Most commonly for myself, this is the whole BiomesOPlenty folder. (Although there seems to be an ID conflict between DW20's v1.0.8, and higher versions, because 2 more ID's are added.) In this case I just copied the lines of code for the Biome gen's I didn't want, or required.
Finally, copy over the original Server 'world' folder you've been using, the ops text, Server properties file, and the whitelist text files. I say Copy, because all of this should be a testing for conflicts. You don't want to lose your old server.
Now, for the Client. Make a copy of your client folder for your mod pack (or just rename it.) and delete the old one. DL the update you wish to have. And then run it on the server. If there's any Block ID issues, you'll know immediately cause it will tell you. If you play with your keyboard configs at all, you can now just copy the old 'options' out of your FTB/<modpackfolder>/minecraft folder, and paste it into your new one.
Lastly, if you're still getting Duplicate issues, then you missed a step above, or made the most common mistake of dragging & dropping files, rather than downloading new. I have to holler a lot at my less knowledge'd players for this, because it create hours of hassle. "Drag & Drop is for a Portal Gun! Not Files!". lol If you get any issues after this, atleast now you can post knowing that any dup. issues are resolved.
Good Luck,
Griff ^..^/