I think some memory is not added to the memory list util late on in the boot, depending on your card. When I used to use RemApollo for instance there was a hack called FakeLocal that would enable fast memory as "local" memory very early on.
Apart from that OS3.9 uses a LOT of chipRAM compared to 3.1, so you are best advised to use FBlit so that programs and icons etc. use fast memory. But PLEASE read the docs with regard to the special section about OS3.9, rather than coming back saying "Hey! I installed FBlit and now I get gfx corruption and it crashes after a while". Right now on my A1200 with 640x400+ screenmode in 64 cols with WB backdrop, Genesis and AmiDock running I have 1.377Mb free chip which is pretty good going for 3.9
I happen to disagree about going back to 3.1 though, I wouldn't once you get used to AsyncWb, rawWbinfo, defIcons, AmiDock, UnArc and so on and so on being there.
