Ran into something similar.
For me, the button wasn't grayed out. I went to upload the baseline, saw the spinning wheel, but it didn't upload. I did save the work, thinking I'd try again later.
When I went back, the project wouldn't open.
I ended up doing the entire CIS Level 2 for Sequoia over again. This time, thankfully, it uploaded.
Hopefully, you don't have to start over. But if you have the project up, maybe try to copy the work to another Mac?
And now some of the generated .mobileconfig profiles aren't fully (manually) importing into my dev instance running 11.11.1 since I still can't upload from JCE.
Some of the settings in the profiles, based on enabled compliance rules, are missing when I review them in Jamf (I thought maybe it might not be able show some of the settings), nor when I review the profile when installed on test machines. But they're listed in the .mobileconfig file created by JCE. So either Jamf isn't reading the files correctly, or the file is malformed somehow? Or some 3rd issue?
I've attached the contents of the generated .mobileconfig viewed in terminal, and what the target test machine shows the restrictions applied by the .mobileconfig as installed by Jamf.
Sounds like it could be a permissions issue.
I had the same problem after the app updated to v1.4
My fix was the following:
1. Deleted the app from the Applications folder
2. Downloaded new installer.pkg from Jamf Compliance Editor
3. Installed the new .pkg
Then when I opened my project the button was no longer greyed out and I could upload successfully.