Ok, so I've had some problems in the past with characters floating in the air and Anyone using Empty's mod will have cried themselves to sleep with the characters sinking halfway through the floor, but I just discovered the solution. It's a question of scale.
If the FPE scales the character to greater than 100%, then the character will float above the floor, if the FPE is less than 100% the character will sink below the floor. The further the number is away from 100%, the greater the sink/float will be.
I realise this may be an issue only effecting Empty's MOD users, but I know alot of people stopped using the mod because their characters were sinking, and many of the videos demonstrating the video were using stock characters, (who are all scaled to around 92%).
scale up the FPE to 100%, delete the .bin and .dbo files for the character and you'll be fine.
Peas
Butters