This is related to a change that was made in the latest ZK version, which I will continue to say is both non-intuitive and utterly stupid.
Storages now hold only "reserve" metal. The 500 metal placed in a storage will only be used by
A)Morphing units or
B)Constructors set to high priority.
There are two ways to fix this:
1)STOP BUILDING STORAGE. If you are excessing metal, build more constructors/labs/nanos to use that metal. Metal sitting in storage is only wasted.
2)Bug the devs until they revert or fix this change. It's a major noob trap that could be solved by adding a toggle switch to storages that would turn on the reserve feature. *IT SHOULD NOT BE ON BY DEFAULT*