If it was only happening during certain scenes I figured it would be a problem with post processing or some other advanced features. Some one else would possibly know more than me on this issue.
However you can try to re-install Aali's custom driver to see if that helps.(this may be a newer version than in remix patcher also.)
http://backup.ninjaloot.se/share/ff7_opengl-0.7.5b.zip
To install just extract to your final fantasy folder. Then run ff7config and select custom driver. Edit the ff7opengl.cfg again and set all the parameters and see if that helps.
I think the remix patcher can only be run by the driver coming with it namely 0.7.3 version of Aali's version. And Tenken he meant changing the red text here.
# ff7_opengl config file
# use shaders, if available and supported
# turn shaders off to use the OpenGL 1.1 backend
use_shaders = yes
# plugins
# a movie plugin is required, the music plugin is optional, but required to make FF7Music work
movie_plugin = plugins/ffmpeg_movies.fgp
music_plugin = plugins/ff7music.fgp
# vertex and fragment shaders
vert_source = shaders/main.vert
frag_source = shaders/main.frag
# YUV fast path shader
yuv_source = shaders/yuv.frag
# post-processing shader, used to apply fullscreen effects
post_source = shaders/bloom2.post
enable_postprocessing = yes
# display frames per second counter in upper right corner
show_fps = no
# display some real-time debug information
show_stats = no
# set the window size (and fullscreen resolution) of FF7
# 0 means use original resolution (whatever ff7.exe provides)
# preserve_aspect adds black borders as needed to preserve a 4:3 aspect ratio
window_size_x = 1360
window_size_y = 768
preserve_aspect = yes
fullscreen = yes
# prevent glitches due to rounding errors by rendering in the nearest (larger, if supported)
# multiple of the original resolution and up/down-scaling
prevent_rounding_errors = yes
# check your driver settings if this option doesn't seem to work
enable_vsync = yes
# limit snowboard, coaster and highway minigames to refresh rate / 2, i.e. 30fps for a 60hz display mode
# vsync must be enabled and working for this to have any effect
minigame_framelimiter = on
# same thing, but for the battle swirl
battleswirl_framelimiter = off
# replace FF7's default framelimiter timer source
use_new_timer = yes
# use a more stable (but less accurate) timer to control FF7's framelimiter
# this option has no effect unless the use_new_timer option is on
use_stable_timer = yes
# allow FF7 to use linear filtering for its textures
# some things look slightly better with this option on, but alot of textures just lose their detail
linear_filter = on
# make all dialog boxes transparent, same effect as the transparent dialog boxes YAMP patch
transparent_dialogs = on
# expand battle viewport to cover entire screen and make the battle menu transparent
new_battle_interface = on
# enable alpha blending for textures without an existing blending effect
fancy_transparency = on
# store external textures in a compressed cache for increased performance
# compression is not lossless, some artifacts may appear when this option is in use
# texture cache does NOT update automatically if the source image changes, however, deleting anything from the cache
# will cause that file to be recreated from the source
compress_textures = yes# read files directly instead of using LGP archives
# this option requires you to have all your LGP archives unpacked in direct/, with one folder for each archive
# for example; if FF7 is looking for aaab.rsd in char.lgp, this option will make it open direct/char/aaab.rsd instead
# this option should be used for testing only, performance will take a hit
direct_mode = off
Its not in your .cfg file so you may be using older drivers. If you're not using the remix patcher I absolutely advice you to use 0.7.6b. If you're using remix patch then tough luck.