I have also experienced this exact problem when trying to build a newer
version of Filelight (1.0 is not in the repositories yet) and xsidplay
(to get libsidplay2 support).  I get failures upon trying to overwrite
/bin/ld.

Upon examination of the filelight .deb, I noticed that it also included
all the files the above poster listed, and a couple of files from my
home directory in the .qt configuration settings.  I have no idea why it
decided it needed to do that either.  Most of these extraneous files,
such as /usr/bin/ld, had zero size.

Now, in the case of xsidplay I've done it often enough I actually made a script 
to do most of it for me.  This script was unaltered, and worked before but does 
not now. 
In the case of Filelight, I downloaded the new source and the source deb 
currently in the repositories (from which I copied the debian/ folder) and ran 
./configure and then checkinstall -D.  The configure appeared to work perfectly.

-- 
checkinstall cannot install
https://bugs.launchpad.net/bugs/115107
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