I don't have experience with any errors in timezone configuration in WeBWorK, so I don't know if I can be any help. I just installed 2.10 on one of our servers, and set the timezone in the site.conf file, not in the course configuration. I don't know what would happen if you had a different timezone in the course configuration and site.conf file, but wonder if that's what's happening here.
For whatever it's worth, the timezone in the default sites.conf.dist is America/New York.
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Trouble with dates and times and timezones
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