I have a portal site CompanyPortal and a couple of sites CompanySys,
CompanyAc, CompanyHR.

Indexing happens every night (Full). I can search documents if I run a
search on CompanyPortal (i.e. http://CompanyPortal), however if I search
being at the site i.e. http://CompanyPortal/sites/CompanySys, the search
result comes back empty and asks me if I want to search through
CompanyPortal site.

Can any of you shed light on why isn't the search not working.