Mojo, as I'm sure you know d/l speeds are usually server/traffic or maybe local disk capacity issues. I went with d/l for BFD3 and existing expansion packs for a new install, was 2-3 hours tops.
To your original issue, came across similar issues when attempting to load and run older projects done with BFD2. I installed BFD2 -after- BFD3 and it downgraded the license manager to an older version. Issues -seemed- to be related to the FXpansion license manager trying to run on project load when it didn't recognize the previously authorized content. After a bit of trial and error, was able to get things running with the latest license manager. But took several attempts.
FWIW, you shouldn't have to reload the audio to fix the problem. Just make sure you scan for content and confirm authorization before trying to use it. And a big +1 to twaddle's comments on running as administrator and confirming the audio engine BFD thinks it wants to use. Hope the latest go proves to be the charm, but noted a number of BFD2 crashes when running older projects in X3, almost always related to adjusting a kit piece parameter while the transport was running. Thinking I'd better work this out before a client asks to revisit an older project.
HTH.