I've gotten mine to work ok under Ubuntu 11.04 (Ecrap er.. E-Machines 250G), and have the same thing happen as previously posted (RTG vs. Native). The frameskip helps alot, though its a compromise between updates and playability for games and such (I get robbed alot playing Pinball Fantasies ALOT that way, even more frustrating when my nice wide-screen LCD TV with VGA input can't sync to PAL refresh rates, and I'm limited to emulation to see anything on the bottom of the screen for s/w written in Europe). The audio also kills things alot, aside from AHI stuff. Win-UAE seems to work well on the wifes setup, aside from native audio getting garbled alot.
Anyway, don't know if this'll help, but I'll C&P my .uaerc file (Ubuntu).
config_description=AmiKit configuration (2 MB chip, 128 MB Z3 + 32 MB RTG)
config_hardware=false
config_host=false
config_version=0.8.29
amd64.use_tsc=no
sdl.use_gl=true
alsa.device=default
alsa.verbose=false
unix.rom_path=~/
unix.floppy_path=./
unix.hardfile_path=~/
unix.savestate_path=~/Amiga-Emulation/
unix.cpu_idle=0
x86.use_tsc=no
sdl.map_raw_keys=true
use_gui=yes
use_debugger=false
kickstart_rom_file=/media/DATA/UAE/ROMS/Kick31.rom
kickstart_ext_rom_file=
kickstart_key_file=$(FILE_PATH)/
flash_file=
cart_file=
kickshifter=false
floppy0=
floppy0type=0
floppy1=
floppy1type=0
floppy2=
floppy2type=1
floppy3=
floppy3type=1
nr_floppies=4
floppy_speed=100
parallel_on_demand=true
serial_on_demand=true
serial_hardware_ctsrts=true
serial_direct=true
scsi=true
scsi_device=/dev/sda
sound_output=normal
sound_bits=16
sound_channels=stereo
sound_stereo_separation=7
sound_stereo_mixing_delay=0
sound_frequency=44100
sound_interpol=none
sound_adjust=0
sound_volume=0
sound_latency=100
comp_trustbyte=direct
comp_trustword=direct
comp_trustlong=direct
comp_trustnaddr=direct
comp_nf=false
comp_constjump=true
comp_oldsegv=false
comp_flushmode=hard
compforcesettings=false
compfpu=true
cachesize=16384
joyport0=mouse
joyport1=joy0
bsdsocket_emu=true
synchronize_clock=yes
maprom=0x0
gfx_framerate=8
gfx_width=640
gfx_height=512
gfx_width_windowed=640
gfx_height_windowed=512
gfx_width_fullscreen=1024
gfx_height_fullscreen=600
gfx_refreshrate=0
gfx_vsync=true
gfx_lores=false
gfx_linemode=double
gfx_correct_aspect=false
gfx_fullscreen_amiga=false
gfx_fullscreen_picasso=true
gfx_center_horizontal=smart
gfx_center_vertical=smart
gfx_colour_mode=32bit
immediate_blits=true
ntsc=false
hide_cursor=true
show_leds=true
keyboard_leds=numlock:none,capslock:none,scrolllock:none
chipset=aga
collision_level=playfields
fastmem_size=0
a3000mem_size=8
z3mem_size=128
bogomem_size=0
gfxcard_size=32
chipmem_size=4
cpu_speed=max
cpu_type=68040
cpu_compatible=false
cpu_cycle_exact=false
blitter_cycle_exact=false
log_illegal_mem=false
catweasel_io=0x0
kbd_lang=us
state_replay=no
state_replay_rate=250
state_replay_buffer=20971520
hardfile2=rw,dh0:/media/DATA/uae/hdf/amikit.hdf,32,1,2,512,1,
hardfile=rw,32,1,2,512,/media/DATA/uae/hdf/amikit.hdf
hardfile2=rw,dh1:/media/DATA/uae/hdf/gcc.hdf,32,1,2,512,1,
hardfile=rw,32,1,2,512,/media/DATA/uae/hdf/gcc.hdf
hardfile2=rw,dh2:/media/DATA/uae/hdf/games.hdf,32,1,2,512,1,
hardfile=rw,32,1,2,512,/media/DATA/uae/hdf/games.hdf
filesystem2=rw,hd1:Ubuntu:/,0
filesystem=rw,Ubuntu:/
filesystem2=rw,hd2:Win7:/media/Win7,0
filesystem=rw,Win7:/media/Win7
filesystem2=rw,hd3:WinXP:/media/WinXP,0
filesystem=rw,WinXP:/media/WinXP
filesystem2=rw,hd4:Data:/media/DATA,0
filesystem=rw,Data:/media/DATA
input.config=0
input.joymouse_speed_analog=20
input.joymouse_speed_digital=10
input.joymouse_deadzone=33
input.joystick_deadzone=33
input.mouse_speed=100
input.autofire=10
input.1.joystick.0.disabled=0
input.1.joystick.0.axis.0=JOY1_HORIZ.0
input.1.joystick.0.axis.1=JOY1_VERT.0
input.1.joystick.0.button.0=JOY1_FIRE_BUTTON.0
input.1.joystick.0.button.1=JOY1_2ND_BUTTON.0
input.1.joystick.0.button.2=JOY1_3RD_BUTTON.0
input.1.mouse.0.disabled=0
input.1.mouse.0.axis.0=MOUSE1_HORIZ.0
input.1.mouse.0.axis.1=MOUSE1_VERT.0
input.1.mouse.0.axis.2=MOUSE1_WHEEL.0
input.1.mouse.0.button.0=JOY1_FIRE_BUTTON.0
input.1.mouse.0.button.1=JOY1_2ND_BUTTON.0
input.1.mouse.0.button.2=JOY1_3RD_BUTTON.0
input.2.joystick.0.disabled=0
input.2.joystick.0.axis.0=JOY1_HORIZ.0
input.2.joystick.0.axis.1=JOY1_VERT.0
input.2.joystick.0.button.0=JOY1_FIRE_BUTTON.0
input.2.joystick.0.button.1=JOY1_2ND_BUTTON.0
input.2.joystick.0.button.2=JOY1_3RD_BUTTON.0
input.2.mouse.0.disabled=0
input.2.mouse.0.axis.0=MOUSE1_HORIZ.0
input.2.mouse.0.axis.1=MOUSE1_VERT.0
input.2.mouse.0.axis.2=MOUSE1_WHEEL.0
input.2.mouse.0.button.0=JOY1_FIRE_BUTTON.0
input.2.mouse.0.button.1=JOY1_2ND_BUTTON.0
input.2.mouse.0.button.2=JOY1_3RD_BUTTON.0
input.3.joystick.0.disabled=1
input.3.joystick.0.axis.0=JOY1_HORIZ.0
input.3.joystick.0.axis.1=JOY1_VERT.0
input.3.joystick.0.button.0=JOY1_FIRE_BUTTON.0
input.3.joystick.0.button.1=JOY1_2ND_BUTTON.0
input.3.joystick.0.button.2=JOY1_3RD_BUTTON.0
input.3.mouse.0.disabled=1
input.3.mouse.0.axis.0=MOUSE1_HORIZ.0
input.3.mouse.0.axis.1=MOUSE1_VERT.0
input.3.mouse.0.axis.2=MOUSE1_WHEEL.0
input.3.mouse.0.button.0=JOY1_FIRE_BUTTON.0
input.3.mouse.0.button.1=JOY1_2ND_BUTTON.0
input.3.mouse.0.button.2=JOY1_3RD_BUTTON.0
input.4.joystick.0.disabled=1
input.4.joystick.0.axis.0=JOY1_HORIZ.0
input.4.joystick.0.axis.1=JOY1_VERT.0
input.4.joystick.0.button.0=JOY1_FIRE_BUTTON.0
input.4.joystick.0.button.1=JOY1_2ND_BUTTON.0
input.4.joystick.0.button.2=JOY1_3RD_BUTTON.0
input.4.mouse.0.disabled=1
input.4.mouse.0.axis.0=MOUSE1_HORIZ.0
input.4.mouse.0.axis.1=MOUSE1_VERT.0
input.4.mouse.0.axis.2=MOUSE1_WHEEL.0
input.4.mouse.0.button.0=JOY1_FIRE_BUTTON.0
input.4.mouse.0.button.1=JOY1_2ND_BUTTON.0
input.4.mouse.0.button.2=JOY1_3RD_BUTTON.0
Also, did a few screegrabs that might be easier on the eyes.
