I don't know about the shrubs, but I'm going to guess that you had food sitting out and/or left in the fridge since before you installed BV. All old food is corrupted and must some way be deleted. Old food put into the fridge can cause all kind of freaky behavior due to the corruption. You can thank EA and Maxis for this feature.
Heres the odd thing, the left overs I had BEFORE BV come out fine and they don't disappear... but whenever I put NEW leftovers in after BV then get them out, they disappear into thin air.
I've played 5 different families post-BV. No problems with leftovers or gardeners. Have you tried taking out your downloads folder and seeing if the problems still exist?
Haven't tried that because all the hacks I have are by JM or twojeffs and they are all updated for BV. Will try it though.
Any time you install a new expansion, all food is shot. To prevent the shooting of food, you will need one of the Director's Cut hacks, "Don't Shoot Food". This will prevent your food from being shot by new expansions, although food that has already been shot will not be saved.
Remember, don't shoot food!
I will download that one for use with the next EP so my food aviods Dick Cheney... I mean Maxis.