I filled in a contact form on the Banco De Espana website. We will see what they say. In the meantime I did more investigating with the notes that I have.
Did you know that they made changes to both the obverse and reverse of these notes?
I used the Oxford Image Comparison tool to make a composite GIF:

When they darkened the collar frill and jacket they also darkened the eyebrow and made the beard more dense on the side. They extended the shadow also towards the middle of the note.
Here's the reverse:

On the reverse also the eyebrow was darkened on the side and the beard was changed slightly. The right side of the moustache is lighter.
But the biggest difference is the registration device. On the note with the light collar, the colours are pink and green but on the dark frill they are blue and pink:

Now, I found a similar situation where a note was issued in 1992 and then changed, mainly by darkening and reissued in 1996. This is the 2000 Pesetas note, where I only have the 1996 issue.
But have a look at a toggle of images I found online:

The later note from 1996 has been darkened similar to the dark frill version of the 1000 Pesetas note. Especially around the face, the process is similar.
This makes me think that the light frill 1000 Pesetas note was issued in 1992 and the dark frill 1000 Pesetas note was issued in 1996.
Either way, it seems the 1000 Pesetas note will have to be split, just as the 2000 is. I am just waiting for confirmation that the light collar was issued in 1992 and the dark collar 1996.