I seem to be encountering something of the same problem, but perhaps not quite as pronounced. Recently installed BP with the three mega mods and I remember it wasnt happening at first, when I started in Irenicus dungeon, only after I have been playing for a while. Same thing there is a slight pause every second or so but it you pause the game via spacebar the jerkiness is gone.
// Log of Currently Installed
WeiDU Mods
// The top of the file is the 'oldest' mod
// ~TP2_File~ #language_number #component_number // [Subcomponent Name -> ] Component Name
~SETUP-BD-
TOB.TP2~ #0 #0 // Baldurdash Fix Pack for
ToB, v1.5
WeiDU
~SETUP-BD-
TOB.TP2~ #0 #1 // Textupdatepack -> Baldurdash English Text Update Pack for
ToB, v1.4
WeiDU
~SETUP-SOS.TP2~ #0 #0 // Shadows Over Soubar, v1.11
~SETUP-SOS.TP2~ #0 #1 // Remorhaz walking speed adjustment (for ENGLISH version .EXE ONLY!!!)
~SETUP-
TDD.TP2~ #0 #0 // The Darkest Day, v1.11
~SETUP-TS-BP.TP2~ #0 #0 // TORTURED SOULS v6.04.01 (BP Compatible Version)
~SETUP-BPV177.TP2~ #0 #0 // Big Picture AI/Enhancement Mod, version 177
weidu (beta)
~SETUP-BPV177.TP2~ #0 #1 // Improved Suldanessallar
~SETUP-BPV177.TP2~ #0 #2 // Improved Spellhold
~SETUP-BPV177.TP2~ #0 #3 // Wand of Orcus Add-In
~SETUP-BPV177.TP2~ #0 #4 // Improved Small Teeth Pass, by Kensai Ryu
~SETUP-BPV177.TP2~ #0 #6 // Kensai Ryu's Improved Crypt King
~SETUP-BPV177.TP2~ #0 #8 // Improved Random Encounters, by Gebhard Blucher and Kensai Ryu
~SETUP-BPV177.TP2~ #0 #9 // Gebhard Blucher's Lich in the Docks
~SETUP-BPV177.TP2~ #0 #10 // Red Badge, Poison-Based Encounter, by Westley Weimer
~SETUP-BPV177.TP2~ #0 #12 // The Ritual, by Westley Weimer
~SETUP-BPV177.TP2~ #0 #15 // Ascension for BP
~G3TWEAKS.TP2~ #0 #197 // Add Ammo Belts and Potion Cases to
SoA
~SETUP-BP-
BGT-WORLDMAP.TP2~ #0 #0 // Revised worldmap for the Baldur's Gate - including coloured Baldur's Gate map icons -> Installing new Worldmap for use with Mega Modification
~SETUP-BP-
BGT-WORLDMAP.TP2~ #0 #2 // Use new worldmap for Throne of Bhaal as well
// Recently Uninstalled: ~SETUP-GUI.TP2~ #0 #0 // Game Graphical User Interface (GUI) -> "Original
SoA/
ToB"