I think I found out what the problem is:
The flyovers always happened with A-6s, never with A-7s or F/A-18s. I checked the A-6E_79_LOADOUT.ini, and to cut a long story short, I learned that the MK82 Snakeye BaseQuantity is set to 12, and the Strike loadout equips 20 of them! Thus, the A-6s' inboard racks (which should have been loaded with 8 Snakeyes) are instead loaded with 8 CBU-100 AT cluster bombs. The AI does not drop these on buildings or other targets of Strike missions, and thus the A-6 flights do not expend all their ordnance, and somehow the AI reads this as "target not destroyed, keep flying." I went into Objects/Weapons/MK82SE/MK82SE_DATA.ini and adjusted the "BaseQuantity" value from 12 to 20 (BaseQuantity=20) I started a new campaign today and I haven't had a single problem. To anyone reading this, go into your Objects/Weapons folder and check your BaseQuantity values if you're having the problems I described.