Please have a look at my workunits :

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176388677
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176388673
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176317120

All finished with "Rosetta score is stuck or going too long. Watchdog is ending the run!" and scored incredibly high !!!!

Please have a look at my workunits :

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176388677
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176388673
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=176317120

All finished with "Rosetta score is stuck or going too long. Watchdog is ending the run!" and scored incredibly high !!!!

Don't worry, this is standard Rosetta beta behaviour.

Your configured runtime is 1 hour (3600 sec.). If your computer receives work units where the first model needs more than 4 hours (4 x configured runtime) to complete, Rosetta will finish computing after about 4 hours 15-30 minutes and award you 80 credits for your crunching efforts. You receive 80 credits regardless of your actual computing time.

It is an effective way to boost one's credits, but the results are scientifically worthless - and such work units are not sent on to other crunchers and are dead to the world. For these reasons it might be advisable to increase the configured runtime a bit, even if you lose credits this way.