I have the exact same issue.
updated through stardock central today from 1.03 to 1.04 and just started a small random game.
after updating
all my graphic / sound / effect and player options where gone (
except for my custom keyboard-settings...
also the market was 3:1 with all rates like 1.03 and 1 weird thing i have never seen before:
but maybe that's just a rare normal thing?
it really looks weird when ships jump between those two
*edit
I just downloaded the 1.04 version from the website and installed it on top of my current 1.04 from stardock - which fixed the bug with the old market values!when I launch stardock it says there is an update available (1.04.022) where I "only" have 1.04 installed and it asked me to update...
so something is broken with on of your updates ...