I have had this issue for years and have never been able to solve it. 

This issue only occurs with assemblies created from step files.  Creating the step file goes fine and i save the newly created assembly along with its parts into a chosen folder.  Some time later as i am working on my job multiple instances of the parts, never the assembly, will appear (seemingly) randomly in other folders within that job.  I have never seen it jump outside of the file structure of the job i am working on.  This leads me to believe that it is being saved in the folder of the current parent assembly i am working on, when i save that assembly.  The files are not being used by the original assembly and i can delete them but then they will reappear later.

I have contacted my VAR and they have worked with Solidworks directly.  I have done complete new installs with new templates only to have the issue return.  2 of my coworkers have seen this as well but i don't see anything online relating to this issue.

Has anyone else seen this? 

Thanks In Advance