Same issue, it seems that the lines:
if sys.argv[1][:4] == 'pdf:' and version >= 0x060206:
opts = '-define pdf:use-cropbox=true ' + opts
in the script /usr/share/lyx/scripts/convertDefault.py cause a *LOT* of trouble
All pdf Graphics reappear after commenting those two lines
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lyx cannot display graphics or math preview images
https://bugs.launchpad.net/bugs/513853
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