clashing note columns

[David Bobroff]

In a piece I'm doing in LilyPond I have a lot more single-staff 
polyphony than I've dealt with before.  I'm getting loads of:

warning: ignoring too many clashing note columns

The *output* looks fine.

Example: http://notendur.centrum.is/~bobroff/lily/measure.png

The 'd' in the half-note chord is tied over from the eighth note and is 
in the upper voice.  If I don't flip the stem direction the stem is up 
and the note head offset.  If I flip the stem it lines up as in the 
original (shown in the link) but I get the warning.  Should I just 
ignore this and put up with the warnings?  It is, of course, more 
important that the output look good, but I'd also like a 'clean' 
LilyPond run, too.

-David