Hi,
What internal resolution for flycast are you running? I'm using 800x600 and output at 1080p, core resolution (no integer scaling) have no issues running dreamcast games at all, apart from WINCE (windows CE) games as I'm using the recently reverted flycast core, these are not currently supported. Check you are using alsathread for audio and turn of shaders, as most shaders are too demanding (I do use 2x presale bilinear/zfast on all games without issue). Oh and check you are using recent BIOS files as well.
Here's parts of my config:
reicast_alpha_sorting = "per-triangle (normal)"
reicast_anisotropic_filtering = "4"
reicast_boot_to_bios = "disabled"
reicast_broadcast = "Default"
reicast_cable_type = "TV (Composite)"
reicast_custom_textures = "disabled"
reicast_delay_frame_swapping = "disabled"
reicast_div_matching = "auto"
reicast_dump_textures = "disabled"
reicast_enable_dsp = "enabled"
reicast_enable_naomi_15khz_dipswitch = "disabled"
reicast_enable_rttb = "disabled"
reicast_fog = "enabled"
reicast_force_wince = "disabled"
reicast_frame_skipping = "disabled"
reicast_framerate = "fullspeed"
reicast_gdrom_fast_loading = "disabled"
reicast_hle_bios = "disabled"
reicast_internal_resolution = "800x600"
reicast_language = "Default"
reicast_mipmapping = "enabled"
reicast_pvr2_filtering = "disabled"
reicast_region = "Default"
reicast_render_to_texture_upscaling = "1x"
reicast_synchronous_rendering = "enabled"
reicast_system = "auto"
reicast_texupscale = "disabled"
reicast_texupscale_max_filtered_texture_size = "256"
reicast_threaded_rendering = "enabled"