What Amiga 500 board revision do you have? Mine sees the RTC in the trap door expansion. It also says "Oki" in the menu. Your ACA500 doesn't see the trapdoor RAM at all, maybe that is the issue. Mine shows 512 Kb in the menu for "Trapdoor slow ..." Do you have the trapdoor RAM switch turned off maybe? Most have a switch on them to turn off the trapdoor expansion. Regarding the RTC, your battery might be dead as well, they only last 3-5 years I believe, unless you have a battery that isn't soldered in and replaced it recently.
Update: Oh wait, you state you think it's Rev 6 above. I would pop the top and look myself, you only need to lift up the right lower corner of the RF shield to see after removing the keyboard.