So there is this small white rectangle that is flickering on my screen in game. It isn't that bothersome but I would rather fix it because it's distracting. Sometimes it will happen when I start up the game (and continue while I play) but sometimes it won't. I also have flickering fog of war which could be related but I didn't fix that because it wasn't bothering me much.

If anyone can help it would be greatly appreciated!

Also I'm using the widescreen mod, fixer, and unfinished business mods.

There were some flickering issues, especially under Windows 8 or on high resolutions when using the widescreen mod.
Try Aqrit's DDrawFix
http://bitpatch.com/ie_ddrawfix.html

Extracted it into Torment Game folder (same place as the .exe)
Edited the aqrit.cfg so that:
ForceDirectDrawEmulation = 1
NoVideoMemory = 1

Aqrit also made a variation to fix graphical glitches with the fog-of-war, which might be worth a try as well.
http://www.shsforums.net/topic/56441-proof-of-concept-alpha-blended-fog-of-war-pst/#entry559817

As a workaround, check if it's better when you minimize or close all programs, activate auto hide for Window's taskbar and disabling slideshow desktop wallpaper (if enabled). Then start the game from a desktop shortcut.

It seemed to fix itself for some reason. I noticed that whenever I opened the game and I had Chrome up it would happen.If I open the game up when I don't have the tab open it works so that's pretty weird lol. Thanks a lot for replying ill check out the fog of war fix.

All the better :-)
There's a good chance that Chrome indeed caused the problem. There have been several cases were Chrome interfered with games, but they don't occur regularly.

Windows10 here. I tried closing Chrome and the larger flickering white rectangle disappeared, however the active icons in my notification tray are still showing through whenever they blink. Any clue about how to fix this? I tried enabling Auto-Hide on my taskbar, and this made the icons disappear, but there's a tiny white bar where those icons would be that blinks whenever their background activity updates. Very distracting! :/

Ok, I just have to remember to minimize all windows with active graphics (E.g. spinning loading wheels on browsers, etc.) And to use auto-hide on my taskbar so the active notifications don't steal focus from PST. Working clean so far now.

So I was really struggling but finally I managed to get it working without any issues.

I'm on Windows 10 x64 and main issue was flickering when moving to edges of map.

1) Installed GOG version through Galaxy client
2) Run setup-ddrawfix.exe to remove forcing of ddraw rendering
3) Complete the whole MODs setup process (Widescreen, UI, fix, tweak, ub)
4) Added modified ddraw.dll from here (this helps also with not streching videos, keeping aspect ratio)
5) Removed intro videos following [url=http://pcgamingwiki.com/wiki/Planescape:_Torment#Skip_intro_videos]this[/url]
6) Compatibility on Torment.exe: Disable display scaling on high DPI settings

So thx for pointing in right direction =))

Thanks a ton for that ddraw.dll link, that fixed both the annoying fog of war shimmer and the background window/taskbar pop-in on Windows 10.

I have to go deep-diving into Google for that stupid file every. single. time I play Torment. It's absolutely mind-boggling that there are only a few links to it across the internet, and that other than that blurb a few posts up, no one has included it in their "You'll Never Guess What Planescape Mods Work Best" lists or whatever.

Looking at various screenshots of peoples' games, I assume that maybe native 1920x1080 is just too big for them by default, so they probably drop to a lower resolution where scaling and buffering make flickering LCD pixels a non-issue... but I've never seen a native screen NOT have the flicker, and there's always a gaggle of comments arguing about it being v-sync, a user configuration error, or that it doesn't happen to them, so it can't actually be a problem.

Idiots.

I'm going to make sure I save a copy of it along with the rest of the mods, because I know i'll forget about it.

It really should be a part of any essential mod list.