I think I have answered my own question, please verify that this is correct:

A GC cycle is the time from the GC start to the GC end.  The % Time in GC is
only updated at the end of the GC.  The % Time in GC indicates the time it
takes for the current GC cycle as a percentage of time between the current
and previous GC ends.

The following represents GC cycles over time.

             GC1
GC2
-------+------+-------------------------------+---------------------------+
        start       end                                           start
end

           0         1                                               2
3

The points in time 0-1 indicate the time taken to perform the first Garbage
collection (GC1).  The points 2-3 shows the time taken for the second GC
(GC2).  The % Time in GC counter is only updated at 1 and 3.  The value of
the counter at point 3 is the time taken between 2-3 divided by the time
taken between 1-3.

Mark