Hi Thierry,
load dominodefrag mail "-a -c -i -d" is the same as load compact mail "-a -c -i -d" when doing a compact. From my testing it would appear that using -a options prevents the ODS from being upgraded to 51. Trying load dominodefrag mail "-c -i -d" worked, but doesn't do the archiving.
DominoDefrag just uses the standard compact options. See for more information >>> http://publib.boulder.ibm.com/infocenter/domhelp/v8r0/index.jsp?topic=/com.ibm.help.domino.admin85.doc/H_COMPACT_OPTIONS_1761_STEPS.html
So this is not a DominoDefrag defect.