I and running Version 5.4.11 boinc
The packet shows rosetta version 5.4.0
Packet Name
PSH_0130_looprlx_GP120_OD1_138_146_6419_1415_29_0

Currently running

THen I have a stack with two rosetta 5.4.1
ready to run

Running Asus P5wdg2-ws
930 775 cpu
2 GB Memory
XP Pro

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There was an issue with Rosetta 5.40 where it would try to perform a checkpoint just before completing a work unit. And then sometimes immediately after the checkpoint, but before completing the WU, BOINC would decide to spend time on another project for a while.

This has been corrected with Rosetta v5.41. ...but if you are saying that the WU shows 100%, and a status of running, and it accumulating CPU time, then that is something different. If it remains in a state like that for more then an hour or so, I'd suggest suspending the WU. Then later let it run again and see if it doesn't finish out on it's own. If not, I'd abort it.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/