Unfortunately there is a bug in 2.4 with fast HD. We will definitely get that fixed in 2.5.
I apologize for the trouble.
Yes, the separate files are supposed to work like this. The camera cannot write files larger than 4 GB.
Using the Edge 800 and a VIRB Basic should work if you record in 1080p. It's hard for me to tell what might be wrong without having access to the files. If you can somehow make these available to me (maybe via sharing them on Dropbox) I'd be more than willing to take a look.
But we are definitely looking into alignment for 2.5, there seem to be a few things off.