I had not done this quest prior to the I completed them together, transcribing the cube and then grabbing the scroll. Before continuing the Dawnguard quest with the scrolls I went back to Septimus and gave him the cube, and he told me to collect the blood.

The problem I am having is that the extractor isn't working. When I kill one of the target races, activating them goes straight to their inventory, bypassing the hidden perk that is supposed to bring up a menu to extract the blood. So, needless to say, I cannot continue the quest.

I have disabled all plugins one by one including the Unofficial patch, everything except Skyrim and Dawnguard.

Not sure if it matters, but just for clarity, I was a vampire at stage 4 throughout all of this, with Serana as a companion. She was the one that turned me, before entering the Soul Cairn.

For anyone else having this problem, I was able to bypass the blood collecting and continue by opening the console and entering:

SetStage DA04 50

Still, it would be nice to be able to play as intended.

Wondering if anyone else has experienced this, when doing things in this specific order. I saw another bug post that mentioned the crossover of these two questlines, so there might be an official patch-worthy issue here. Still able to replicate it without mods installed, and have no problem with other mods that use hidden perks, as this quest does to generate the extraction menus that aren't showing.

Off hand, two bits to check. make sure your character is getting the hidden perk 00079af5. The other aspect, is check your loose files / scripts.

After you uninstall those mods, in your data\scripts folder are there any files with da04 in the name?

Could it be a glitch with Namira's ring maybe? That forces a similar menu to pop up when trying to loot a corpse.

I'm currently experiencing this and originally thought that I just had to beat the dawnguard storyline to fix it but no dice. It's still not working. I think im going to CC it.

Dawnguard really shouldn't impact it any. The only thing Dawnguard changes is the name of the Elder Scroll to Elder Scroll (Dragon) [and add an option to buy the scroll back from Urag].

It sounds like either a loose script being left over, or some mod has a script running in your game still that's impacting the harvest script. The later would really svck, because it's a difficult problem to fix [well, mostly I don't know how to approach fixing it].