> MAME 0.72, ClrMAME 3.05a and a problem: scanning operation does not see any of
> new systems' roms. However they were properly rebuilt

do some of these:

1) don't use a datfile, use profiler's -> use emulator binary to create a dat (or whatever it was called)
2) don't enable Scanner->Advanced->allow not separated biosfiles...same for rebuilder
3) be sure the biossets are in an active rompath
4) be sure all systems are enabled
5) clean your cache
6) scan with all check and set + roms options enabled