Hi Alejandro,
I will try different version of DS-5 at weekend. I have tried only different MQX4.1_Vybrid. With that it behaves same way. Same version of DS-5 just for Linux with MQX4.2 it is working just fine.
I think it is problem with debugger or file that it uses for its settings probably from MQX4.2. I can transfer my compiled code to SD card and run it. When I use Baremetal project I am able to debug it, transfer it to SD card and run it. Yesterday I was working with that Baremetal project and it works fine but when I ran this project today it is behave same way as other projects. I have few Eclipse based IDE's. I am using these IDE's each for different type of project. Is it possible that this could be the cause? Could they affects its settings for projects or for them selfs somehow?
I am attaching warnings and errors from different example project with MQX4.2, DS-5 v5.23.1 win7:


I do not know if it is related but I have also problem with cloning MQX4.2 library. I have tried that on two PCs both with win7. I have compiled MQX4.1 without problems. Details are in thread below:
Cloning Wizard MQX4.2 Vybrid error