the emmc has two partitions for data.. one is the large MyDocs partition that you see when using mass storage mode.. its also all the data you see when using the file manager on the phone..

but there is a second partition (2gig) for /home/user and /opt. this holds all your installed packages (that are correctly optified) and all your settings/data like browser cache, email content, conversations database, calendar..

The two are seperate because when the phone is in mass storage mode and connected to the computer it cannot share access with the computer.. it has to disconnect itself from the MyDocs storage..

If your settings and data were on there, things would be bad and you wouldn't be able to use the phone whilst in mass storage mode..

The down side is you can't see this magical partition when using mass storage mode.. though you might be able to mount it if you had a linux pc.. dunno not tried..