One of my users has an Exchange 2000 Server mailbox, and he's trying to delegate access to a resource mailbox on an Exchange Server 5.5 server. When he adds the resource mailbox as a delegate, the related permissions are reset to none. Why is this the case?

This functionality is by design. You'll encounter the problem you've described if the resource mailbox's external account field in Active Directory (AD) contains the SELF Security Descriptor (SD) because the account can't use the SELF SD. However, the user can assign a regular mailbox as a delegate because the associated account doesn't contain the SELF SD and thus won't be disabled.