I imagine it's supposed to have something to do with Auto Start and/or Auto Initialize. The Symantec fellows could probably speak better to it, but here's a post from AnaMan from 2012:
Auto Initialize option is responsible for automatic loading a proces [sic] models (from *.model project files) into memory, deserializing them and transforming into execution objects. Its purpose is to shorten the time needed for response during first request directed to process after it was published or restarted.
In theory...
Because this functionality seems does not work. I have done many tests and I've never got any sign that auto loading of models had occured.
I did some tests and found that whether I had Auto Start and Auto Initialize checked or not, there was some app pool polling that's going on behind the scenes that eventually picks up the monitoring test project I published.
By manually invoking the web service as you did, you forced a recompile, and thereafter it should repeat on the schedule as intended.
Here's some more info, again, from 2012, from reecardo:
Auo-initialize [sic], I believe, just preloads the flow into memory. I always have it checked, but I don't think it's required.
Another, from 2009 (reecardo):
Auto Initialize, in a sense, "preloads" your project in the workflow engine. It's probably not on by default for the reason of having multiple WFs "preloaded" on a server could be pretty memory-intensive.
Also, here's an interesting read from what seems to be an old, obscure text from the 6.x-7.0 days:
...set the project to Auto-Initialize under the Publishing tab. This will force the project to be recompiled automatically when IIS is restarted and periodically if it is detected that the project is not initialized already. This is a per-project setting. This doesn't remove the .NET requirement that the project be initialized, but it makes it much less likely that a user accessing the site will end up waiting for this process to complete.
And last, but perhaps most helpful, from stuper2 in 2010:
If you rt click on the task tray man and pick 'Settings' you'll find a section called "Worfklow Server Configuration"
On the next popup you'll find "Auto Trigger Info" and "Manual Setup Info" back to back.
These two things participate in auto start workflows. Under Auto Trigger Info you'll find the polling interval (default 1440) that the tool uses to actually look for new auto start workflows that haven't been previously found. On restart (as Mr. Rob M) describes, this is run so restarting the Workflow Server service effectively resets this timer and voila, your auto start gets found and registered.
Alternatively you could shrink this auto poll interval OR, add your auto start project to the list of manually triggered projects at which point the auto registration is irrelevant.