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Okay, I've fixed the issue but I am still happy I created this thread so everybody and Rui would know that such a problem may exist.
My sound files were in one folder and the projects was in another. Both folders were in a QTractorSessions folder where I save everything, so all relative paths were correct.
On the old system, where the project was created, it was loading okay although the project file was in one folder and samples in the other. On the new system, however, QTractor seemed to search for samples in the folder where the project was in and could not find audio files.
What I did was edit the paths to the audio of every clip, that partially helped but the clips sort of reloaded and so all my editing of clips' lengths were gone - the audio maximized all clips.
So then I just took the project file and put it into the same folder with the sound files. Then it worked.

I think the way session project is created - the dialogue - has a potential to screw locations like this, because when you save midi clips and audio files, you are asked to save them in a location and so you create a folder for them, but saving a project file is not synced with that and you save it, not realizing that saving a session project is not saving it into the dir you have specified before for midi clips. You know what I mean?