I have had this problem for about a month now. I have a single service with 6 individual layers. Some would show up in the attribute table, some would not. I noticed it was the layers with high numbers that would not appear in the attribute table widget. I decided to republish with a higher number under the parameter 'Properties' -> "Maximum number of records returned by the server:'
My highest table is 21000 so I made it 25000, and WALLA. All my layers now show up in the widget.