are you definitely stereo throughout? you may be getting phase problems, stereo music squeezed onto a mono recording can sound pretty gash.
Also make sure the volume control on your MD player isn't set to high, it may be peaking which your sound card won't be able to deal with
there's something wrong somewhere if you are not getting 'the full picture' and no amount of EQ tweaking will help.
If it's important to you then get a cheapish external soundcard with proper gain controls on it
I have an old NETMD usb minidisc player you can have for next to nowt if i can find all the bits, this will do the transfer digitally