Closed loop cooled cpu still running hot??

I would say its not working at its best.
Please tell us how you have it setup as well as how the case's ariflow/fans is setup.

Which air cooler did you have? The H100i isn't better than the huge air coolers (e.g. Noctua NH-D14), but it's much better than the stock Intel cooler.

Is there a path for the heated air to dissipate into the room and for fresh cooler air to enter the case? I've had people think they can put the pc into a cabinet or closet because its liquid cooled...

How much thermal paste did you use?

Sounds to me like you should buy some Arctic Silver 5 thermal paste, take off your cooler, and install it again.

Assuming that the cooler is working properly, it isn't making flush contact with the cpu, or else you forgot to clean off the CPU nicely when you installed the H100i.

Here's what to do

You'll probably want to get some thermal paste cleaning solution and a set of micro fiber cloths to get things super-clean before reinstalling the cooler. Here is Arctic's cleaning solution for removing thermal paste. And here are some micro fiber cloths (if you don't already have a few). Isopropal alcohol will also work, but the solution I linked does a better job.

Use the first solution on a paper towel to clean all the visible stuff from the coper cooler plate on your H100i and on the CPU itself. Once it looks clean, use the second solution with a micro fiber cloth. You'll notice a bunch of stuff accumulating on the cloth that you couldn't even see. Once the cloth stops picking up stuff (while using the second solution), the surface is clean.

Now get the Arctic Silver paste ready by warming it up. The best way to warm it up is to put it in a zip-lock bag (with no extra air in it), and then put the bag into warm water for about 5 minutes. Hot sink water is all you need. Don't boil it!

After the paste is warm, put a pea-sized dot of Arctic Silver 5 in the middle of your CPU while pushing the tube down on the middle of your CPU (prevents air bubbles, which are bad).

Make sure you have the bracket for the H100i installed on the back of your motherboard facing the correct way. It can install backwards but not allow good contact, which results in poor cooling like you have now. Then install the cooler plate on the CPU and screw it down snugly (i.e. tight but not so tight you muscle it).

Go do something else for a while so that the paste can set. Give it an hour or so. When you come back, try running Prime 95 on SmallFFT while watching the temperatures. If you did everything right like I described, you should have normal temperatures. Poor temperatures after this procedure probably means you have a bad cooler that you should return for an exchange.

Good luck!