Did you try any other settings - any change in sound then?
Could be a number of things. Always pays to check that all cables go where they're supposed to - red to red, black to black etc. (sorry, I can't tell from your posts how "hifi savvy" you are). How do you connect speakers and sub to the Marantz? Looking at the subs manual, I would follow figure 3 as it is the simplest - sub out from Marantz to LEFT line in on the sub, then speakers from Marantz to your Bostons.
Distance between speakers and yours from them, position of sub, room acoustics all could and do affect to some extent what you hear. Check sub's phase setting.
Instructions in 610's manual seem fairly reasonable though I would start like this, once all properly connected: sub's volume at zero, 603's volume at "normal" - whatever it is to you and Response 1 selected; sub's low-pass filter to "In"; line and speaker level input to zero (note: speaker level should always be kept at zero as you are not connecting to sub's speaker posts, only to line in); low-pass frequency to 60; EQ to A (the manual is not clear about what B does - I suspect these are two different roll-off settings); bass extension to C (lowest), phase to zero. Then gradually start increasing the line in level on the sub until you start hearing the extended bass. If still not happy with it, try changing the phase to 180 etc, etc.
When properly set, sub should integrate with the sats seamlessly - you should only just keep the sub's volume high enough to hear it extend the frequency range from the satellites - anything higher and it is destined to go boomy...
Maybe someone else has another idea, but also think about the possibility that something is not working as it should - if new, you should be covered by warranty. Contact the person/dealer you bought it from for advice?