I have some servers connected to the a storage and all of a sudden, I discovered that after rebooting the server, it looses connection with the storage unless a manual rescan is carried out on the server to check the luns mapped again.
When using FCP, and if the LUNs are mapped to your hosts WWN, it's up to Windows to rescan and map the LUNs to drive letters or mount points.
Things that can mess this up could be if you are presenting the LUNs to more than one server at a time, which is normal in a Cluster server, in such a setup the LUNs are SCSI locked by one of the Cluster Nodes, and cannot be accessed by any other, unless if its the Quoum disk.
SCSI locks can be a bitch to remove, but one thing which allways works is to reboot all the nodes involved.
Since you haven't mentioned Clustering at all, I suspect this is not your problem ?
One thing I would suggest is to update to the latest Host Utility from NetApp and latest SnapDrive and MPIO driver. Microsoft's updates could overwrite some options set by one of these utilities, upgrade or reinstall might fix it.
Also I would try to install HBAnywhere or SAN Surfer (for the HBA) which allows you to have a better look into what the HBA can see... here are also some options you can set for the HBA drivers which may help you...
It's a lot of stuff to look into I know, but basically I would start with the NetApp utilities reinstall and see how it goes...