Comment 2 for bug 1537282

Mint 17.3 Cinnamon 64-bit - exact same situation. Delete all instances of Spacer app, remove Spacer app from panel, reboot, add Spacer app to panel, new instance becomes the n+1 instance of the previously removed instances which have all reappeared.
Multiple occurrences of the Spacer app cannot be manipulated. Adding more than one instance "stacks" the spacers on "top" of each other, and when an attempt is made to move the spacer(s) in panel edit mode, the spacer stack with all instances will be moved to the new location but attempting to add another instance adds the spacer to the relocated "stack".