I have very little experience with VGA 666 (in fact, I tried for first time today... ^_^U) but I have no problems with any emulator. I can give you some advices, maybe it works with you, if you still have problems.
Set dpi_mode in hexadecimal format, in your case 0x10 as it's listed in this table, just in case:
dpi_mode=0x10
Set framebuffer to your desiere resolution:
framebuffer_width=1024
framebuffer_height=768
Comment any HDMI config line:
#hdmi_force_hotplug=1
#hdmi_group=1
#hdmi_mode=1
#hdmi_drive=2
Kept this lines commented:
#dtparam=i2c_arm=on
#dtparam=i2s=on
#dtparam=spi=on
Or if you want, uncomment turning off everything:
dtparam=i2c_arm=off
dtparam=i2s=off
dtparam=spi=off
Try some other VGA modes, like 75hz (0x12) or 800x600 (0x09, 0x0B).
Be sure emulators are not using special scaling resolutions than may be incompatible.
Last one, universal solution to any computer problems: install retropié again and try with default retropié configuration.