I am reviving this old thread because I just experienced the same problem with my new G-44 purchase and wanted people to know that the problem still exists.
I purchased my copy of G-44 through the PC Aviator website two nights ago and was exited to install my new payware G-44. When I tried to load it in FSX-SE, I immediately experienced a CTD. After much cursing and hair pulling, I eventually came across this thread.
I located my panel.cfg file and confirmed that the duplicate entry in the VC section still exists. I believe my download is V1.1
Should Flysimware not have made correction by this time, or is the PC Aviator website still hosting an older version?