Automation Apps not present when toad is launched

Is it possible that you had multiple Toads running at the same time?

If so, they could have stepped on each other while writing ToadActions.dat

You can avoid this by using the /VIRTUAL switch on your scheduled actions. This will cause the scheduled run to make a private copy of the user files folder.

FWIW, another user reported a similar problem a while back and reported back that /VIRTUAL helped him.

Just add /VIRTUAL on the command line call to Toad in the scheduled runs. There are some options with it (details in the help file) , but I think /VIRTUAL is all you really need.