Am unclear ... please clarify what:
'updating one of the programs with some new files' means.
Uploading files ... to moodledata/repository/[somenameofrepo] is that correct? Were the files uploaded via ftp and was binary transfer used to upload?
Example of one of the file names you are uploading? Any characters in the name like '/' or spaces?
And what did you check ... 'checked the repository'? Can see them, but what of file permissions/ownerships?
'spirit of sharing', Ken