You can upload the entire battery at once by selecting "upload" and then clicking on the battery marker (a flag if vehicles are showing, otherwise a symbol with a single straight line over it) twice. This will distribute the ammo in the manner which best "fills out" the gun sections. This can relieve you of the micromanagement of individually selecting flatracks and ammo carriers.
If this does not solve your problem, e-mail your saved game (from the Savegame sub-directory of the install directory) to:
[email protected]
with a DETAILED description of the problem you are seeing and we will be happy to check it out.