How to reproduce:

- get the gcc sources (I took them from SLES9)
- quilt setup gcc.spec

> find . -depth -name "series"
./gcc-3.3.3/gcc/series
./gcc-3.3.3/series

In gcc.spec we have:

%prep 
%setup -q -n gcc-%{gcc_version}
%patch0 
%patch1
cd gcc
%patch2 
cd ..
%patch3
%patch4
[...]
%patch64 -p1
%patch65 -p1
cd gcc
%patch66
cd ..
%patch67
%patch68
[...]

So %patch2 and %patch66 get applied from within the gcc subdirectory and end up
in the gcc/series file.

Problem: depending on the current directory within the gcc sources, quilt
commands like "quilt push -a" and "quilt applied" behave differently.