On my server, the Low grade stack size is set to 1000.   When a player puts over 500 low grade into a electric generator, it will only take 500, and the rest is lost.    I will reduce the stack size back to 500 so players don't loose lowgrade, but want to let you know. 

1. StackModifier in no way shape or form modifies storage container sizes.

2. If you are referring to the small generator in the game it natively only accepts 500 fuel and no more.
    Unless you use some other plugin to try and modify the storage value.

I suggest you look on your server for the other stack modification plugin trying to increase Storage Stack Sizes and let me know which one is causing the bug.