Well, let's see...
When I ran the flatten transparency method under Object > I was seeing the floor grid drop out, and the wall grids drop out... I hope this was what you were refering to.
At any rate, a bit of organizing and cleanup seemed to help, at least with the 'dropping' grids.
[ol]
[li]I copied the wall 'Grid' objects onto another layer 'Wall Grid', as they were on an imported or linked image layer before, and normalized their stroke to 2 pts, using the Magic Wand set to .5pt to select out strokes of nearly the same width. Then I converted the strokes to outlines... that stopped them from dropping.[/li]
[li]I remade the Wall Gradients using actual gradients, as they had been converted to vectorized grads, only b/c they added to the complexity/filesize of the illustration.[/li]
[li]I also converted the Floor tile grid to outlines.../li]
[/ol]
You might simply go through and reorganize the objects on their layers a bit, till everything has a place, using Collect in New layer on similarly colored/themed objects, and go nuts converting strokes to outlines in those areas that drop on print.
I printed to a b/w HP 5000GN and didn't notice any missing data, you might look to your printer drivers as a possibility... also, depending on your output needs, rasterizing the whole buggin' thing will ALWAYS force a print... Although PhotoShop often does a better job of Rasterizing AI files than AI does. Naturally.
Sef.
It is alright to decorate construction, but never construct decoration. - Pugin, on Arch.