Yeah, I had already opened a ticket earlier this morning. Turns out that it's not really a bug per se...
Microsoft is no longer adding the path to the mailbox databases to the registry. Instead, they're only including the Exchange Install Path in the registry, which of course is what the SEP client uses to build the auto-exclusions. If you move the Exchange 2010 transaction logs and/or mailbox databases to other drives (which is recommended by MS), the only way to enumerate the paths is through a PowerShell command. Since the SEP client doesn't run that command in the background, it doesn't know the location to the mailbox databases, and can't auto-exclude them.
At this point the only solution is to manually exclude the mailbox databases.