I am using a mod serwer with plugins enable i found that protection plugin are disabling functionality of machines

The issue is same type like that is BuildCraft/BuildCraft#2224

Manly Block placeevent is stopped and Block Placer, Braker don't work tested on them.
Is going Project red to have a support of Permissions or what co called fakeplayer.. or it has and we don know it :)

This is not Project Red's fault as it only tries to place blocks, if it doesn't have permission to it will obviously fail. Use a mod that protects your blocks like the security station of PneumaticCraft