Customize ordering problem

By which method are you trying to do this? The answer may vary accordingly...

 

I've had the same problem with SMBPrefs. I manually make the changes myself.

No matter where in the plist file I move it to, SMBPrefs is always the last thing on my first page.

 

So you're using Customize (rSBT), unfortunately only the apps listed under Dock and Springboard are sorted as you list them, those under Extended Springboard are sorted at random, regardless of your list. The current version of Customize only allows 16 max in Springboard list (change the number in rSBT > Settings > Springboard Icons), hopefully this will be changed in a later version (unless there's some in-built limitation or something).