I would identify whether or not those scheduled deployments are followed with the reported issue. If so this may help Sage identify the cause. I suspect there is a product issue but we have not found anything to shed any more light.
We were never able to identify a pattern with changes to the web app. We have moved the majority of our users over to firefox (which is atleast 3-5x as fast load time as IE) and have set firefox privacy settings to delete cookies everytime firefox closes. We still run into the issue on occassion and typically the issue is resolved by clearing out the task pane filters by selecting "Clear All" while in the group that the lookup fails in.