There are a couple of steps that you can attempt to resolve your issue. Please ensure you have adequate backups before following through with any changes.
1. Check out the Security Log file on C:\ProgramData\Qlik\Sense\Log\Proxy\Trace. If there are any issues with the certificate, it rolls back to the default certificate.
2. on the MMC - (local computer) - personal certificates, right click on the certificate file you installed and select All tasks -> Manage Private Keys. Add the Qlik service account (Account running all qlik services) and explicitly grant full control + Read permissions to the qlik service account
3. You might not need to remove all spaces from the thumbprint value - however you do need to remove the first character if its not readable (paste it into a command prompt window to see the 'invisible" character).
4. (If you cannot access the QMC at this stage to update the hash - you might have to use as postgres client to access the database and update the ssl thumbprint field in the ProxyServiceSettings table.
5. Stop all Qlik services. Open a command prompt with admin privileges and run C:\Program Files\Qlik\Sense\Repository\repository.exe -bootstrap
6. Start the Qlik services.