I experienced the same issue. With the switch fully disabled from offline, after an NSP is added with the update, some games will still have the Pop-Up Menu even if the game is fully updated. I found the remedy be:
1. install the base Version of the game using goldleaf.
2. After installing v0 of the game, exit Goldleaf.
3. Select installed game that had pop up menu. Click on the game and atttempt to open it and show the pop up. Click play on the game. DO NOT HIT DOWNLOAD.
4. Exit the game after it boots
5. Open Goldleaf and install the game Update.
I hope this works! It bothered the crap out of me. I am not sure if this trick works on the newest update. I was running 9.0.1 when performing all of this.