I was having the same issue. Mine turned out to be that although I had set the parameters in the php.ini file, and checked the max limit in the apache configuration file, I still could not upload large files. Upon checking the ssl_error_log, I received the below message:
[Fri Feb 20 11:02:00 2015] [error] [client 10.3.251.104] ModSecurity: Request body (Content-Length) is larger than the configured limit (13107200). [hostname "moodle.example.org"] [uri "/repository/repository_ajax.php"] [unique_id "VOdoiM3K-W8AAHwbvPcAAAAB"]
SecRequestBodyLimit 13107200
SecRequestBodyNoFilesLimit 131072
SecRequestBodyInMemoryLimit 131072
Mod security was not allowing files above a certain limit, so smaller files were accepted. Comment out, remove, or update those lines and restart web the service.