left side placement with buttons starting on the bottom...

Even better, I might have found the cause and a way to reproduce with a new toolbar.

• Create a new toolbar (empty directory) and dock it to the left side in a single column
  
• Create about 5 shortcuts, and put a separator between each of them
  
• Set the appearance of the top shortcut to "Move to bottom"
  (Note: you will see additional spacing before each separator)
  
• Right-click one of the shortcuts near the bottom and 'Hide' it.
  (Note: you will see all shortcuts that were above the hidden button now being drawn on top of each other)[/list:u]
  So in conclusion: separators (moved to bottom) have extra spacing, and hidden buttons (moved to bottom) cause everything above to be painted on top of each other.