I agree, Eveclean and it is amazing how many organisations still believe that IT systems will always make life easier - in many cases it won't.
Perpetual inventory review is the best way to do this. The alternative of a traditional stockcheck not only results in the whole business stopping for a period of time whilst stuff can't move to allow it to be counted in only one place, but it means you go many months without checking anything.
The bit that appears to be missing from your organisation is the feedback loop from Quality Assurance. What should be happening is that the results from perpetual inventory checks, if good, result in a lowering of the number of checks done (and vice versa). It is all about gaining confidence in the control and accuracy of the stock numbers. There's no point continuing to count stuff if it is rarely incorrect. That's what World Class organisations do.