Apparently X3.3293 has VGA support, but it had some issues - the release notes suggest that the output was YUV instead of VGA, and it had other issues. The release notes also suggest that you need to reset the X3 to default settings as you switch from 3293 to 3294, so switching between the two is unlikely to be clean.
Try one of the other VGA Bioses on a separate bank. X2.5035 is a good choice, but you don't need the BFM version - just flash the standard version to banks 5 and 6 on your X3. Have a search for FrostyTheSnowman_Xman954_X2_5035_VGA_BIOS_v1.0_fixed.zip in the usual places.