Missing config files when building for linux

I am building a linux headless server and it used to work fine.

Then I updated from 4.3.2 to 4.5.1. I have not tested yet to check out the project from scratch and go back to the old version will solve my issue. (since I would like to stay on the new version)

After building there are several files missing. In the datafolder/Mono/etc/mono only a file called 'config' is there.

The last working build had also the folders '1.0', '2.0' and 'mconfig' contained. In these folders are some config files, especially a file called 'config.xml'.

The program will not start, however if I copy all the files over from the last working build, it starts and runs just fine.

Does anybody know why the files are missing in my linux builds? Or has some pointers in the right direction??

Thanks a lot in advance! :) :)