I have found different machines behave differently. On the laptop I have just updated to Zesty if I shut down the native Linux BOINC. and then start the one under wine, I get a message about needing to start boincmgr from the same directory as the client. A little investigation showed that closing the manager left the client running and from a terminal kill 999 then enables the wine version to run.

No problems doing it the other way around.If I can come up with anything to stop this minor irritation I will post again.