It says SKSE is not running because you SKSE64 installation is incomplete and SKSE is not, in fact, running. Just because it shows a SKSE vbersion in-game and in response to getskseversion soes NOT mean it is fully installed or running- all it means is 1-3 of the required 60+ files are installed.
Here, once again, is how to install SKSE64 into SSE correctly:
Firstly, it's easy to configure Vortex to install ALL OF SKSE64 into your game with only about 10 seconds of extra config work. Here's how to do that:
Installing Script Extenders With Vortex. There is also
a tutorial video but the author was apparently late for an appointment or whatever, so be prepared to stop it at the important spots so you have at least a fighting chance to read what he's doing.
If you're not using Vortex or do not wish to take the 10 seconds required to do it, then you will need to do a manual installation of SKSE64:
1. Choose the correct version of SKSE64 to match the game version you are using- here is a list:
Game / SKSE64
1.5.97 / 2.0.17 (Current versions as of November 20, 2019)
1.5.80 / 2.0.16
1.5.73 / 2.0.15
1.5.62 / 2.0.12
1.5.53 / 2.0.10
1.5.50 / 2.0.8
1.5.39 / 2.0.7
1.5.23 / 2.0.6
1.5.16 / 2.0.5
1.5.03 / 2.0.4
2. Install SKSE64 manually:
2a- Download the SKSE64 7z archive to your desktop
2b- Extract the SKSE64 7z archive to your desktop
2c- Open the top folder of the SKSE64 extracted archive
2d- Copy the SKSE64 archive's Data folder, skse64_n_n_nn.dll, skse64_loader.exe and skse64_steam_loader.dll
2e- Open your Skyrim Special Edition main folder, ..\Steam\SteamApps\common\Skyrim Special Edition
2f- Delete any and all files you see there that begin with "skse."
2g- Paste the 4 objects you Copied in Step 2d into the open SSE folder
2h- Authorize the folder merge with the existing Data folder- if you already have a Data folder and do not get a Data folder merge warning, try to find and delete the files you just pasted into the wrong location and start over, this time reading these instructions more carefully. If you do NOT already have a Data folder, meaning SKSE64 is the first mod you have installed, you will not get a folder merge warning and that's OK.
2i- Authorize all Script overwrites
3. Right-click the new copy of skse_loader.exe in your Skyrim Special Edition folder
4. Select "Send to" then "Desktop (create shortcut)"
5. Close your game folder and the extracted SKSE64 7z Archive folder if they are still open
6. Manually launch Steam (if it is not already running) using the Steam shortcut
>>>NOT<<< skse64_loader.exe.
7. With Steam already running, double-click your new skse_loader.exe shortcut to launch SSE with SKSE64 properly installed
8. Later, when Vortex tells you there have been external changes and asks for guidance, be sure to select "Save All Changes" so Vortex does not undo anything you just did
9. Never again use the Mod handler of the vanilla game launcher because it will disable SkyUI_SE*
10. Always and forevermore make sure Steam is already running before you launch SSE via skse64_loader.exe
*You can eliminate this restriction by adding Skyrim.esm as a Master to SkyUI_SE.esp
