As i have had a similar issue going on and bc i'm relativly new to DF i went through alot to insure i didn't sound like a noob before coming here, and now beleive its time to ask the experts.
When the game first began i designated a site near the soon to be dug entrance to my fort as a catch all storage location. At first all went smoothly, all the food, items, weapons, etc etc all managed to be transported there with the exception of a few items which i blew off at the time as there not being enough storage space at the time.
However as time went buy and i completed digging out my new home and prepared a proper storage space, i proceded to get rid of my temporary storage space at the entrance and designated the new one in its proper location......
however the barrels at the location of the cart remained, and only 1 item (an empty barrel) was placed in the food pile. This proved quite aggravating and after checking on here to see if there was a quick fix i proceeded to attempt to the best of my ability to solve it myself.
My first attempt was the remaking of the pile several times. This had no result.
being a Noob i thought mayhaps it was a distance issue that the dwarves would not collect something so far away. after designating several more food stockpiles betwixt the initial cart and the final stockpile i had no results.
Next i checked to make sure i had not somehow designated the cart as a stock pile. I had not.
I then proceeded to (being the noob i am) deconstruct the cart, once again to no avail.
I then attempted to see if they were forbidded, being that they were not i procceed to forbid them, give it a moment, then unforbid them, once again, no results.
The next step was an attempt to dump the items in a new zone, this furthermor failed to acheive the desired result.
the last and final action i could think of doing to acheive the result of moving the food was to desgnate the area as a *high* traffic area, mine some near by ore so some hauler would have to come by, and hopefully for some unkown reason see the food and come back for it..... they didnt
so i am now saving and retiring the game for the time being, and starting anew, hopefully myself and igotsmeakabob will get the answer we need, and if none is available then that this will be forwarded to the bug department.