I am setting up a new game. I added GrandMasters of Hllalu, and I got this message at launch:

One of the files that "Grandmaster of Hlaalu.esp" is dependent on has changed since the last save.
This may result in errors. Saving again will clear this message
but not necessarily fix any errors.
One or more plugins could not find the correct versions of the master files they depend on. Errors may occur during load or game play. Check the "Warnings.txt" file for more information.

I saving again, but message still shows @ launch.

GameFile0=Morrowind.esm
GameFile1=Tribunal.esm
GameFile2=GDR_MasterFile.esm
GameFile3=Book Rotate.esm
GameFile4=Weapon Rotate.esm
GameFile5=BT_Whitewolf_2_0.esm
GameFile6=Bloodmoon.esm
GameFile7=Better Bodies.esp
GameFile8=Unique Banners and Signs.esp
GameFile9=UIT_Buckmoth.esp
GameFile10=UIT_Ebonheart.esp
GameFile11=UIT_Moonmoth.esp
GameFile12=UIT_Pelagiad.esp
GameFile13=UIT_TelVos.esp
GameFile14=UIT_Wolverine Hall.esp
GameFile15=ASE Tribunal Expansion.esp
GameFile16=Illuminated Windows.esp
GameFile17=Weapon Rotate - Tribunal.esp
GameFile18=Weapon Rotate - Vendors.esp
GameFile19=SirLuthor-Tools.esp
GameFile20=LadyD_Reduced_Commentary.esp
GameFile21=3S Mannequin.esp
GameFile22=Lgnpc_SN.esp
GameFile23=TravelingMerchants_v2_3.esp
GameFile24=constance1_0.esp
GameFile25=Wayfarer's Rest v1.21.esp
GameFile26=Nevena's Twin Lamps & Slave Hunters 1.5.esp
GameFile27=DB_Attack_Mod.esp
GameFile28=t_lostheir.esp
GameFile29=AtmosphericSoundEffects-3.0-Tribunal.esp
GameFile30=NPCMove.esp
GameFile31=Hendalf_Gold_v.1.3_ENG.esp
GameFile32=Key Replacer Trib & BM.esp
GameFile33=Kahleigh's Retreat v1.1_BMTB.esp
GameFile34=Weapon Rotate - Bloodmoon.esp
GameFile35=ASE Bloodmoon Expansion.esp
GameFile36=Illuminated Windows - Bloodmoon.esp
GameFile37=CompanionTeleportation.esp
GameFile38=B79_RacersRoost_v1.1.esp
GameFile39=frostmoth_repaired_v0_31.esp
GameFile40=The Imperial Legion Badge.esp
GameFile41=Librarian with Jackets & Rotate BM Trib.esp
GameFile42=Grandmaster of Hlaalu.esp
GameFile43=Clean PJM Themed bowsets.esp

Do you have Wrye Mash? You can easily update the plugin to fix this.

Basically, the error means that the plugin was created with a different version of Morrowind to the one you have. The filesize of morrowind.esm is recorded in the plugin's file header and that recorded size and the size of your copy of morrowind.esm don't match. Hence the error.

My standard Wrye Mash thingy: (point 2 is what you're after)

Firstly, initial cleaning of your installed mods:
(1) On the Mods tab all mods should have a green checkbox.
(2) If any mods have a yellow checkbox, select them and then look for the
Save button in the bottom right. Click that and the mod file will be
updated and the error removed. The error just means that the mod was
created with an earlier version of Morrowind to the one you're using.
Saving in Mash will update this version info.
(3) If you have any mods with red checkboxes then you do not have a ESM
file needed by that mod loaded. Check the mod's readme.

Secondly, cleaning your savegames:
(4) Onto the Saves tab, select the savegame you want to fix.
(5) When the savegame is selected the list in the bottom right will be
populated with the mods currently associated with the savegame.
(6) Right click the column headers ("File" and "Num") and choose Sync to
Load List (this will change the mods associated with the savegame to
match those currently selected on the Mods tab).
(7) Click Save
(8) Right click the savegame and choose Repair All.
(8a) Optionally, right click the savegame and choose Remove > Debris Cells.
(9) The checkbox for the save should now be purple.