Not sure but here are some things to think about.
I’m tooling around with this functionality. If I mix physical products and donwloadables in an order and then play around with shipping the physicals and even partially shipping the physicals it has no impact on the links status --- it stays at “available”. Even if I invoice out of sequence with the partial shipping it didn’t impact the link status.
Now, in my sandbox testing I’m placing orders using Purchase Order Payment type which goes into Pending status. I have downloadables set to available at order Pending status. If I put a transaction that is Pending (link = available) on “Hold” the link moves from available to pending. If I then “UnHold” the order the download link goes back to available.
I wonder if your Authorize.net is occasionally putting transactions on Hold which somehow messes things up? For example with Amex transactions?
I also see the 1.2.1 release notes saying “Changed logic of enabling purchased links (now it depends on order item status, not entire order status”. I don’t know what it means but it may mean that the download link status was being ill effected by overall order status. May be this is your issue? It may also mean that once you test out the 1.2.1 release you might resolve the issue. But since you didn’t see the issue without volume production, there is no telling.
You might consider paying for varien support incident so you can get a more direct answer as to whether this behavior is already known and fixed?
Best of luck and congrats on the go-live.