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Hello friends! I am trying to finish the Crimson Nirnroot quest. I was last in Blackreach a couple months ago and was able to enter it through the gate next to Alftand. I went back today, and there was no option to open the gate! I had to go through Alftand again, fight all the damn monsters, and wasn't able to spend a whole lot of time in Blackreach because I was bored with it by then. Unless I am not looking in the right places, I have only been able to collect several crimson nirnroot at a time, so Blackreach has turned into a dungeon I have to keep going back to. But now, my access to it has been blocked. I will give up on finishing this quest and the lexicon one if I have to keep going back through Alftand. I know the route but it is long and fighting the monster is damn annoying. Has this happened to anyone else? A bug? I was able to access it before! If anyone knows of an alternate route that would be wonderful!

The Tower of Mzark is probably the quickest way in and out of Blackreach, but I believe you have to unlock it from the Blackreach side. There are also a couple of other elevators. See this excellent map on this site:
http://images.uesp.net/a/ad/SR-map-Blackreach.jpg

You are definitely not searching enough.You can get all Crimson Nirnroot in under 30 min and if it's your second time there it should be even faster.
There are 3 entry points into Blackreach(Alftand, Mzinchaleft, and Raldbthar) and four exit points(Great Lift at Alftand,Great Lift at Mzinchaleft,Great Lift at Raldbthar and The Tower of Mzark)The exit points are,as their names describe,lifts that are activated if you use one of them to leave BR.
After you activate them they become easy and quick access points between the surface and Backreach so that should be your means of getting there.