Within DVDProfiler it is not possible to have the same profile more than once.
There are ways to circumvent this limitation though.

In your case I suspect the problem to be an incorrect profile identifier (EAN / DiscID).
The normal case for boxsets is that the sub-profiles (Children) don't have a EAN but the DiscID as identifier (There are exceptions, but I don't think that this is the case here).

So for the boxset content:
- Check if the films have separate EANs
- If not: check in the profile if it's listed by DicID (DVDProfilermenu: DVD -> Change EAN...)
- If not: Insert the disc into your computer's drive and click on "Use DiscID of inserted disc"

When finished the EAN should be free again for your separate copy.

Sadly not,
in this case you'd have to create a Manual profile for your single disc.

For doing this go the DVDProfiler menu "DVD -> Add to Collection... -> Add by Title" and unflag the "Download from Invelos"-Option.

Now you have an empty profile with the title of your choice.
To fill it with data you may copy it from the matching profile in your boxset.

If you just want to note that you have 2 of the same DVD, you could always change the "count as" tab to 2 (in the personal information section). You wouldn't have two profiles, but it'd show that you have two copies.