I have a A1GX, in an Acer with a Ali M1429G, maybe it have some similarity :
I do have a Ti486DX2 66Mhz or 100Mhz(cache won't work at 50mhz fsb, need faster chips)
You only mentioned benchmark is Speedsys Memory Throughput, here mine with corresponding FSB speed : I get 24MB/s (33fsb), 16.9MB/s(40fsb) and 25.5MB/s(50fsb).
1 - There is no setting for the cache except "Enable/disable" in the first page of "Advanced System Configuration". If the option is gray-out, Go in "Basic system configuration" and disable "Auto configuration mode and fast boot mode".
2 - Only use 33Mhz or 50Mhz BUS. That one is also important. Setting to 40 or 50 include setting a divider on the memory/isa bus so if you set 40Mhz, the memory will slow down, like if you set it to 25.
3 - If cache is enable and properly set with the jumper and it's not showing, then it is likely that one of more of youre cache chip are defective or that something is wrong with the cache related parts/traces on the board.
I have extracted the VBIOS of my BIOS too and I plan to try other BIOS and swap it too once I get my hand of some eprom and a competent programmer, That BIOS is just too anemic and there is no memory adjustement options. The only cool thing with it is that you can CTRL-ALT-ESC from DOS and go in the BIOS without rebooting, shame the bios is so crap.
In any case, test you're cache SRAM and stay clear of 40Mhz bus speed.
Edit : If there is no cache option at all in the BIOS, it's likely to be automatic, system test it at boot and enable it if it pass the test. There is no need an option as if it's enabled and there is no cache, it will detect there is no cache. The option in the BIOS is more... To disable the cache, when you have cache.
Edit2 : You are right about the 3.3V, you don't seam to have a voltage regulator on that board. The A1GX do.