Different behavior between vault versions when deleting file

[MikiWatts]

Hi, we've recently upgraded our vault version, and I've noticed a difference in behavior when deleting files in VS. In the previous version, when you'd delete a file from the project, the file would be removed from the project and there would be a delete file operation in the Pending Change Set, and I was able to include it in the commit and merge it to other versions later on.
Currently with VS 2015 I'm getting a window that lets me choose between deleting the file from source control and / or leave the file in the working folders, and a do nothing option that leaves the files in source control.
The problem is that if I select the first option, the delete takes place immediately without a delete file operation in Pending Change Set, and if I select the second option, then the file will not be deleted from the source control.

This causes either files getting deleted but not being able to merge them to other versions, or not deleted at all from source control, and ending up with junk files in source control in either case.

What I want is the previous behavior, where it would remove the file from the project and leave a delete file operation in Pending Change Set.

We've also upgraded from VS 2010 to VS 2015, so that might be the reason for the different behavior as well.

[Beth]

Check your automatic commit option in the Vault options. You can get there from the Vault Tools - Options - Check In or in VS Tools - Options - Source Control - Vault Options - Advanced options - Check In. If auto commit is turned on, a delete is committed immediately. If it is turned off, it is not.

[MikiWatts]

Auto commit is not checked. I've checked in VS and Vault client. Out of the 4 options in that screen, only "Require check out before check in" is checked.

[Beth]

Did you upgrade from something older than Vault 6?

The next time you delete, try holding the Shift button. You might have turned off a confirmation window with a setting to delete from Source Control.

[MikiWatts]

Will do. I've checked the Command Dialogs screen, and everything is checked there.