There is an issue with network drives that are set to be mapped on startup, where windows attempts to map them before the network has been initialised properly.
A partial fix for this is to give the computer a static IP address, this works most of the time because it causes the network to be ready faster, but not always and may not be an option.
A better option is to make a scheduled task that runs when the network is available:
Reconnect Network Drives
At log on>
Start a program
/c "net use Y: \\Server\Share & net use Z: \\Server\Second Share"
Start only if the following network connections are available
Another issue is programs that are run as administrator don't have access to shares mapped as a user.
To work around this problem, configure the EnableLinkedConnections registry value. This value enables Windows to share network connections between the filtered access token and the full administrator access token for a member of the Administrators group.
Download and run the following file to make the change to the registry:
Windows Registry Editor Version 5.00 [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System] "EnableLinkedConnections"=dword:00000001