I'm having the same issue. I just tried adding my cert from my PERSONAL/MY store, and the service won't start. In Windows Services, the Rebex Buru SFTP Server Web Admin service can not start. Error 1053: service did not response to the start or control request in a timely fashion.
Through an elevated command prompt, typing "burusftpwa.exe svc restart" results in "Configuration error: While parsing a block mapping, did not find expected key."
If I comment out the lines for the cert from store, and just leave it with http/8880, the web admin service starts fine.
I know my store name and thumbprint are both okay.