Maybe it's me but I'm reading 2 different questions in your post.
Your description sounds like you are using Nautilus to create the share. Nothing wrong with that but are the shares actually gone or is it that the folder icon indicates that it is not shared? Nautilus doesn't keep the share emblem on the icon very well so it may still be shared. One way to make sure though is after the next reboot run the following command to get a listing of the shares:
We are having trouble sharing folders/files that are hosted on the Ubuntu server. I'm able to create a shared folder manually by selecting the folder and configuring the shared options. After creating the shares, other computers can access the data.
The issue starts whenever the server reboots.
After the server restarts, we have to reconfigure the shared folders again.
net usershare info --long
1st, if it's in rc.local then it will be run by root so get rid of the sudo.
I'd like to find a way to mount the shared folders during the boot process. To date, I added the follow command to rc.local file:
sudo mount -t cifs -o username=root,password=XXXXXX //192.168.1.11/ms_SHAREname /media/FC503CC8503C8C00/FOLDERName
Another way is to put it in fstab like collisionystm showed you ( although I'm not sure what group 1901 is ).
2nd, from your description all of you clients to this server are Windows. What is it you are trying to mount? A share on one of the Windows clients?
I get confused a lot so maybe I'm not reading your post correctly.
EDIT: You know, maybe this is the clue from your cifs mount statement:
That's an ntfs partition that you are mounting and based on that mountpoint it looks like you are mounting this manually at every reboot. Is the problem that you want to have that partition automount? That might be the cause of Problem 1. That's easy to do since we already know it's UUID:
 Unmount the partition:
 Create a mount point:
sudo umount /media/FC503CC8503C8C00
 Add the following line to fstab:
sudo mkdir /media/Something
 Then run the following command to test for errors and mount the partition:
UUID=FC503CC8503C8C00 /media/Something ntfs defaults,nls=utf8,umask=000 0 0