This is a rather vague bug report and I dont know if it will be enough to track down the issue. I opened the layout editor on my portal page and created a widget: AMS Article Comments. For some reason this would not render content. Then I moved it around in the side bar to have it change positions. But after that it was gone. No trace of it. I looked in the admincp and there was no mention of this widget.
Have you looked into xf_widget table? The latest one should have the largest widget_id? Widgets should not be deleted during drag and drop.