I suspect that the SQL Server's full-text catalogs may be to blame there, since the searches use FTX queries. You can try rebuilding the catalog by locating it in the Aardvark database (in Enterprise Manager). Right-click each of the three full-text catalogs and select 'Rebuild', then 'Start full population'. Once that's done, check the SQL Server Agent under Management, and make sure there is an Aardvark job for full-text incremental population. Make sure that job has no errors in its' history, that it will run successfully by right-clicking it and selecting 'run now', and that it has a valid schedule.
If the jobs don't exist at all, open the Aardvark program folder, open the SQL subfolder, and run jobs.sql to create the Aardvark jobs on the server.