Hi Leon,
It's late, but hopefully better than never. The latest developmental build of L3DT Pro* supports ordinal padding for the Alpha maps, as requested. After you install the developmental build, you must enable the ordinal padding option by downloading
this patch text file (right-click and choose 'save as'), and then doing a drag-and-drop of the patch file onto L3DT's desktop icon. This patch file ensures that the number written is at least two digits long. If you would like to change the number of digits, either edit and re-apply the patch file, or use the 'Settings->Local settings' menu option, and edit the 'Calc->GenAlphaMaps->OrdinalPadding' setting.
Best regards,
Aaron.
* that's L3DT v2.6d build 12, dated 16th of July 2008.