I'm guessing this is related to the fact that the project is not renamed.
When copying and pasting Script Component A to Script Component B, they both are assigned the same project name. Assuming both Script Components remain in the same package and Script Component B has been altered, the compiled code for Script Component A gets executed and Script Component B does not. I've attached an example so I'd assume "could not reproduce" is not acceptable.
When there are multiple output buffers with several output columns per buffer, the ability to copy/paste components (without undesirable side effects) would be an extreme productivity booster.
This bug has sucked a significant amount of valuable developer hours from my team. Apparently, Script Tasks are also susceptible to this bug. I'm very surprised at the fact that the bug has been known for over 9 years: http://consultingblogs.emc.com/jamiethomson/archive/2005/01/13/SSIS_3A00_-Beware-of-copying-and-pasting-script-tasks.aspx
Hopefully, this can be resolved in the near future.
***Also, the file extension ".dtsx" needs to be added to the allowed file attachment list. I had to add ".txt" to upload the packages.***