Hello!
I have the same issue with the latest client (got it from git at 12.04.2015 - 6PM) the folders are beeing created under the server root, the files are beeing created and have the content. But they get created with pretty useless rights on themselves:
-rw---x--- 1 web1 client3 87 Dez 4 18:25 D5T6yEvvbdWa6SbbjhNFkk-cTWuNK2-AK9ouHOrIs10
-rw---x--- 1 web1 client3 87 Dez 4 18:25 ec0R-UUQXCtVhNmvo8rpl45jCJrili3Qk0HZS3dmfoc
So the files can not be read by apache as the server is in the client3 group but running as the user www-data and not web1; Is there a way to make the letsencrypt client create the files with rw-r–r-- instead of that pointless x for group?
the folder acme-challenge has the same wired permissions
drwx--x--- 2 web1 client3 4,0K Dez 4 18:25 acme-challenge
So as I changed the rights on acme-challenge manually to be drwxr-x— it works! No need to allwo everyone full access on the .well-known folder