I thinks, problem at your config. We have 2 positions to configure.
- At System configuration (Global config). --> If test ok ==> Configuration to remote server is ok.
At your project. We will focus about transfer set: (Source file, Remove prefix, remote directory)
2.1 Source file : if it's blank = workspace directory. in your case i think you should input
**/*
2.2 Remove prefix : refer Here for more info.
2.3 Remote directory: if it's blank = directory that is configured at System configuration above.
Hope it help! Sorry about my English.