* Another thing that WILL screw up your supply is SRing a bunch of units. While your units may hop a train and move at warp speed to their destination, their supply won't. If you Sr a bunch of units into a region, it will take some time for supply to catch up. You should never ever strat-redeploy in areas where you have low supply and have divisions fighting. The redeploying units will carry off up to double their own supply reserve when they move (even if it means leaving the province dry for other units). They will take any supply along the way to maintain this double reserve, thus cutting your supply lines to ribbons. Fuel using units have their fuel consumption set to zero, thus they leave their fuel behind and arrive at their destination with no fuel.
* You can use transport aircraft to dump supplies as close as they can get along a supply route and they'll still be useful. They don't have to be dropped on the troops or an airfield or port for them to get in to the supply system. Anywhere on the route will do. Base them somewhere they have access to a decent amount of supply (supply depot if possible) and select the hex where you want supplies delivered. Watch them, though, as the AI will intercept them if it can.