Thanks CubicWebs, it must have been what you mentioned about the folder. The server, IP and subdomains were exactly the same, but the second time I decided to use a different folder. Re-issuing the license solved the issue.
While the server or IP restriction make sense, I don't understand the logic behind mapping a license to a customer folder... Just out of curiosity, would this be to prevent someone from running two Blesta installations in one single subdomain?
