Here's a trimmed script with some comments.

\version "2.18.2"
\score {

% Begin with a dual staff system -- intro (treble) and accompanying bass.

  { { << \new GrandStaff { <<
         \new Staff { \relative c' { g'1 \break } }
         \new Staff { \relative c'
         { \clef bass
            a2  a4 a    % no anomaly with these notes
%            a2. a8 a   % gets weird with these notes
         } } >> } >> }

% Continue with a single staff, which begins with a pickup note.

    \new Staff { \relative c'
    { \set Timing.measurePosition = #(ly:make-moment -1/8) e8 |
      a1 } } }

  \layout { }
}

As shown - with the second set of three notes under '\clef bass' commented
out - I get this:

[image: Inline image 1]
That's the expected result.  Change the 'a2 a4 a' to 'a2. a8 a' results in
this:
[image: Inline image 2]
That's a dual staff, with the (empty) top (bass clef) continuing (I guess)
from the previous staff system.  (With actual music it continues for the
remainder of the piece.)

It doesn't happen (in my testing) if I remove the line specifying the
pickup note in the lower staff.  And it doesn't happen if I remove the
\score (and \layout) wrapper (which I need for multiple bookparts).

I get the same results on 2.18.2 and 2.19.40.  (This is on Win7, 64-bit.)

-- Lee
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