I'm sure some people set "run logon scripts syncronously" to make logon scripts run more reliably, I know our citrix supplier sets this on their sites and I've found that our logon scripts work 100% of the time with this set, without this set it seems they don't always work. I think in the past this has been due to very slow client PC's though but it's worth a try.
It's more likely to be that the drive is being remembered, do you use roaming profiles?
If you use a vb logon script you could add this section to clear all mapped drives before you map any new drives.
Code:
'Disconnect ALL mapped drives
Set clDrives = WshNetwork.EnumNetworkDrives
For i = 0 to clDrives.Count -1 Step 2
WSHNetwork.RemoveNetworkDrive clDrives.Item(i), True, True
Next or this line to get rid of one line only
Code:
'Disconnect any drive mappings as needed.
WSHNetwork.RemoveNetworkDrive "R:", True, True