Your GM was right... technically... and depending on the details.
And he was right for a reason other than the one he gave.
Your explanation of the situation could be interpreted in two ways. When you say:
"When I affected an enemy with it, my GM succeeded the 1st save"
...if you meant the enemy had already failed a save before the GM made his 1st save, then you are correct. If the enemy had not saved yet, then he is correct.
The rules for poisons are pretty complex and don't provide a lot of explanation. There's a detail about them that isn't intuitive: even if a poison, or any affliction for that matter, requires more than one save to cure, you still resist all of the effects of a poison on the first save.
For example, your Black Lotus Extract requires two saves to cure. Once afflicted, a victim rolls a fortitude save to resist the poison. If he succeeds, he's done. Not afflicted whatsoever. No more saves.
If however, he fails his first save, he will then have to make two additional successful saves in a row to cure the affliction.
The rules for poisons and afflictions cover this, although not clearly. There is a summary at the bottom of the poison's page that covers this detail, however.
I'd say to point your GM to the OGC. If he disagrees then at that point it's a house rule and you'll have to solve the issue through social channels.