I believe that there might be a discrepancy between health and completion values for the T2 Factories. About 75-80% through building, the health bar is already at 100% but the outline is not filled in yet. The only way to get fabbers to assist building once the health bar shows 100% (but the structure is not complete yet) is to have them assist fabbers that were already building, or to reclaim the structure until its health is below 100% then start again.
Actually it's true for any buildings, possible you just notice it with T2 because it's takes longer to build them.
When this happens, try manually telling the units to "repair". If you tell them to assist, which may be the default action, they will just walk up to the structure and stare at it until it's complete, and THEN assist it. So queue repair -> assist.
