I'm going over your preferences file here and I see some problems. Now I don't know how exactly the emulated Mac works per say, but alot of Mac models from the 68k line did not support 256MB of RAM. This may be your first problem, because the actual machine code does not support it.
* ROM: 1 MB
* RAM: 4 MB or 8 MB on motherboard, expandable to 132MB or 136MB using 80ns 72-pin SIMMs; motherboard had 4 SIMM slots which can be filled individually but should ideally be filled in interleaved pairs; can use 4 MB, 8 MB, 16 MB, and 32 MB SIMMs (see 64 MB SIMMs on 68K Macs for information on 64 MB SIMMs)
So I would not use 256MB RAM since I'm sure it can cause some problems. To be honest, 128 is fine for most Macs.....
I run my emulators with FPU off since the Baslisk FPU is still buggy. Use a software FPU instead if you really need it.
I generally turn audio off since it uses up alot of resources and is generally slow and not accurate. (Unless you play games)
In the "Priorities" tab, you have "Frame Buffer" as "above normal"..you are not using frame buffer, you are using direct x, so put this down to normal and move DirectX and GDI up to "above normal" this will speed your refresh rate.
But turn the memory down, a real Quadra 650 does not support 356MB RAM, so I have no reason to doubt the emulator won't.