Hi Mateusz,
Would it be possible to confirm which version you are using?
I was able to set the properties in the codebehind using the same code, the only change I made was adding ReloadData(true). I tested this in v7 with the latest hotfix as you seem to be using v7, please let me know if that is not the case.
protected override void OnInit(EventArgs e)
{
base.OnInit(e);
QueryRepeater1.QueryName = "customtable.SampleTable.test";
QueryRepeater1.TransformationName = "customtable.SampleTable.Default";
QueryRepeater1.ReloadData(true);
}