We do two types of cycle counts.  
 
Based on an ABC analysis, we count the most valuable items, mostly finished goods, fairly often (a few part numbers each week), but we keep stock levels low on these, so it is not time consuming. We do not do standard cycle counts on B or C items.
 
For everything else we do "process control cycle counting", which means that we cycle count them at a critical point. For instance, when we reach the level of our safety stock or kanban reorder point, that is when we compare the system UOH to actual. The safety or split stock levels present a known quantity, so no actual counting needs to be done. We just look at UOH and WIP, and if we have a mismatch we take a closer look and adjust UOH. For other things, like shop stock, we do the count when we receive the item on a PO. We are already stocking the bin, the on hand amount is low, and it is easy to get a good count.
 
This system works very well. We have gone from annual counts that took hundreds of man-hours and showed a 10% variance, down to less than one-hundred hours of time that is hardly missed and which keeps at an audited 99% accuracy. We have decreased our inventory value, increased our turns and seldom have production holds due to stock outs. Happy auditors, happy workers, happy customers. And that makes the Board very happy.  

So, Colin, do you ever use the physical Inventory module to do any of your counting?  Sounds like you just use inventory adjustments.