The words often and constantly do not mean much in this. What you need to investigate is... When does it happen? Does it happen at a server reboot? Happens when you leave the area and come back? When you order something to be crafted? Warped to another dimension and came back? Etc.. Make it easy for yourself and divide this problem in parts, try to see what action or lack of action is needed to make this happen. The more information you have, the easier it is for us to troubleshoot it and find a solution.
To share some experience.. And I bet you, your problem is the same as I will describe below.
I've investigated this issue a lot on a server and in the end it was
always caused by a chunkloading issue. You probably say that's not the case here, but I urge you to check again. On every occasion I investigated this issue, the bases owner told me everything was in the range of the chunkloader.. Until we did find that one ME cable running one block outside the loaded chunks
You can indeed break the controller and put it back, often solves the problem. If not you can try to unload the entire base, wait 5 minutes (make sure a player is not loading the chunks by being nearby) in a remote location and return to the base. This has always fixed the problem for me. Long term fix is to find the part of your ME network that is not in range of the chunkloader.