Regarding possible problems with the transponder in the Honeywell Primus equipped Legacy, here are some links discussing the issue.
http://www.eurocontrol.int/msa/publi...top_press.html
http://www.easa.eu.int/doc/Certifica...Honey_XPDR.pdf
link
To summarize, it appears this rather serious problem has been corrected with a software upgrade, and since this particular Legacy was brand new (i.e. the latest software), I doubt that it had this particular problem.