Different volume for phono vs line level

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That doesn't sound right at all, to me.  When you say the phono stage is set for .5 mV input, do you mean 500 uV (obviously the same, but as far as I can see the configurator doesn't accept input of 0.5 in the mV range so wanted to avoid the possibility of doubt...).  What cartridge are you using, and could you post an image of your phono settings?