And you're using the launcher that came with 2.9.2 correct.
Give me a sec to find the thread with the folder to delete and I'll get back to you, or someone can chime in with the LP fix in the meantime
*EDIT*
Launcher Pro and EB01 S.C. 2.9.
"It's not Launcher Pro and sc 2.9 that don't get along and won't let you save your changes, it's LP and the AOSP launcher that comes with SC. I had the same problem and it was really aggravating me that I couldn't keep the 3D app drawer. Here's what you do. If you don't have Root Explorer, get it from the market. Then open up root explorer. You will see a bunch of file folders listed in alphabetical order. Scroll to data and click on it, then scroll to the data folder on that page and click on it, then scroll to com.fede.launcher, long press on that folder and choose delete from that menu. Then scroll to the top and click on the folder that says parent folder. This will take you back one page, now click on parent folder again. On that page click on the dbdata folder, then click on the databases folder, scroll to com.fede.launcher here too and delete it. Now scroll to the top and click parent folder at the top of each page until you don't see the parent folder at the top of the page and hit the home soft key. Your changes in LP should save now. If they don't after that, a reboot of the phone should completely fix it."