I'm having a similar problem to Samuel
When I enter the ID as a test value in my aggregate or hard code that same ID in a filter, it returns the expected test result on screen. However, when I publish the PDF the dynamic values are all missing.
Having run the debugger, I can see that the correct input variables are coming through to the web screen but the aggregate returns nothing. Even if I run the debugger with the ID hard coded in a filter as before, it still returns no results in the debugger window, despite the test value populating correctly in service studio.
If I simply copy and paste the entire preparation into another web screen, the aggregate returns the expected results. This makes me think that the issue is something to do with the UltimatePDF entry point but this is just speculation.