Ok so I just found a really decent work around to this issue. CMDKEY works on windows 7+ and allows you to enter details into the windows cred manager from the cmd prompt, and if you use the /pass switch it provides its own password entry without exposing the password. It does not present ***** as you type but the password is hidden.
The script below requests the username as normal and creates a var called "%username%" it then checks to see if the cred manager already has an entry for the target server. If it does it just maps the drive to the usename and does not request a password. If there is no entry it then uses the CMDKEY to prompt for password and stores it in cred manager.
set /p username="Enter School Username: "
CMDKEY /list:SERVERNAME | FIND "NONE" > nul 2>&1
IF %ERRORLEVEL% NEQ 0 GOTO MAPDRIVES
CMDKEY /ADD:SERVERNAME /username:%username% /pass
:MAPDRIVES
NET USE Y: \\SERVERNAME\SHARE\%username%