In my experience, the best councils run when there is a good link between the chairman and the clerk, if the mutual respect for each other isn't there then it doesn't work and it sounds like you are doing a cracking job. in response to the agenda item, maybe at the meeting say this item has just come to light and suggest this would require further investigation before any decisions can be made and just ask the clerk why they felt the need to not speak to both yourself and the Vice-chair, maybe there could be some underlying issues with other councillors, bullying etc