No, the Call Server does not care whether it can see a voice gateway.
One of the subsystems that makes up the Call Server is not running correctly - ICM, IVR, SIP. ICM is the main service that connects to the VRU PIM using the MR PIM plug in. It talks to the other sub-systems over the Message Bus, including talking to the VXML Svc for label lookups.
There are a number of things to check, but I would check the PIM. OAMP will show the ICM service in "partial service" if its not connected to the VRU PIM. Is the PIM active?
I would not worry about the file transfers. You can easily use TFTP, and it's typically something you just do once at set up to get the CVP files into gateway flash.
The two problems "could" be interrelated though - I would look at the CVP logs and try to find out what CVP service is not running.
Regards,
Geoff