FTS - Index rebuild causing CPU issues (SQL Server 2008 R2)
Your statement just TRIGGERS the rebuild job, not DOING it.
So - you triggered the job by ALTER FULLTEXT statement, now you can wait until it completes like that:

WHILE (SELECT COUNT(*) FROM sys.fulltext_catalogs WHERE FULLTEXTCATALOGPROPERTY(name, 'PopulateStatus') IN (1, 6, 7, 9)) &gt; 0
    WAITFOR DELAY '0:00:00.1'