Are you using the dynamic core and DOS32A? You also might try setting frameskip=1 or 2 if you can stand it (it will make the game more choppy).

You could also try different output= settings, and make sure you've got scaler=none.

Setting to dynamic core causes the game to crash so it is on normal. I wasn't sure what DOS32A was.
I wasn't to avoid the frameskip because as you said it doesn't make it look that good.
output=surface is definately the fastest and scaler=none compared to normalx2 doesn't seem to make a difference.

Please, there is a SEARCH FUNCTION, if you don't know what DOS32A is you can always look for it.

Considering that you almost have probably the fastest processor that is widely available, plenty of RAM and good enough graphics and sound cards there isn't much you can do with the game to speed it up at this time, unless DOS32/A can help you out. I do believe that the FX models have unlocked multipliers, so overclocking may be in order. Then again, you may have to wait for dual core 64s. I'm not sure what kind of systems they had in mind when they allowed System Shock to use the SVGA (640x400/480) resolutions.

So is there a relationship between clock cycles for dosbox and the Mhz of the processor to work out the optimum level? Is 20000 too high or too low or the optimum setting?

Update: Tried DOS/32A. Causes the game to crash, so no help there.