Sounds like your drills are in excellon1 format that has the drill hits and a report on their sizes rather than in excellon 2 format where the drill sizes are included in the drill hit file.
As for the size, check your output section and ensure that its doing the output at 1:1 for ALL layers.
A tip - on each layer, outside the board edge enter the name of the layer.
i.e. Top artwork, bottom artwork, top silkscreen etc.
This helps to identify them and is good practise.