I don't think you should be using
/mnt in this way. According to the Filesystem Hierarchy Standard;
This directory is provided so that the system administrator may temporarily mount a filesystem as needed. The content of this directory is a local issue and should not affect the manner in which any program is run.
This directory must not be used by installation programs: a suitable temporary directory not in use by the system must be used instead.
A permanent mount, specified in
fstab, should go somewhere else.
Note that current Ubuntu systems use subdirectories in
/media for removable disks, and
/mnt is always left as an empty directory for manual, one-off mounts. I suspect that Ubuntu is enforcing this, or at least facilitating it, by deleting and recreating it on each startup.
I suggest you create a new root-level directory
/network and put your permanent network mounts in there. You may be able to get away with putting them in
/media, but it's probably better to leave that for use by the system. Using
/network as the prefix nicely labels yours as network drives.