I have a repeater table that contains a list table inside of it, both of them have the same query with master detail relationship linked to each other but when ever I tried to run a report it only shows the first selected item in a multi list prompt. where in it should show all the items I selected.
I have absolutely no problem doing what you require. I just did what you said...
First create a repeater table. (Set the Across/Down appropriately)
Go to query explorer and drag in required query items.
Next add the List inside the Repeater table.
Set the Query property of the list to the Query1.
Drag in the fields from Query Items pane as required.
Go to Master details relationships and define the relationship.
Create a multi select value prompt in prompt page.
Set the filter operand as 'in' (check this; i doubt this might be your problem)
Run the report and get exactly what you wanted...