twister: do not set case status on flash timeout

Status was set for testcases after a timeout on flash, which does not
abort the process and continues with test execution and eventually
passes the test.

Setting status on the testcases was done too early and before we have
executed the tests.

Also increase the flash timeout to 60s.

Fixes #45845

Signed-off-by: Anas Nashif <anas.nashif@intel.com>