Here's a fix, though a bit involved.
It requires that you have the Dragon Age Toolset in order to edit your saved game. Make sure you have the latest version 1.01.
Saved games are kept in your "My Documents\BioWare\Dragon Age\Characters\YOUR CHARACTER'S NAME\Saves\"
BACKUP YOUR SAVED GAMES NOW
Open the Toolset and click "File" > "Open File".
Open the saved game you wish to edit (they end with ".das" ).
Navigate to the following...
SAVEGAME_PLAYERCHAR\SAVEGAME_PLAYERCHAR_CHAR\SAVEGAME_EFFECT_LIST
There you will find many numeric sub branches. Each for a specific effect that may or may not be in effect on your character.
Spotting the offending effect requires knowing why this issue is occurring. Each effect is supposed to have a duration "type" defined for it, valid values are from 1-4. (1 = Temporary, 2 = Permanent, 3 = Instant, 4 = Equipped).
The duration type for the effect that wont end will have an invalid value, such as "0" and a duration value of say "20000" that would represent 20 seconds.
Look through each numeric entry at the SAVEGAME_EFFECT_DURATION_TYPE and if it does not have a value of "1" check to see if it has a SAVEGAME_EFFECT_DURATION value greater than 0. If it does, then you have likely found your culprit. Change the duration type to 1, save and play the saved game to see if the issue is resolved.
For those who saved after using the trainer option to try and remove the effect, you may have a problem spotting the offending effect because the trainer changed the effect's duration to 0
If the effect you are bothered by is "War Cry" you can try looking for a numeric entry with a SAVEGAME_EFFECT_TYPE of 1058.
I have been unable to find a list of corresponding ID's/Types to Effect Name, so if you manage to resolve your problem using the above method, please post back with the name of the effect you fixed and it's Type number so others can benefit.
If you want to remove an effect from a party member there are a few ways, the easiest is to let them get knocked unconscious or have them leave the party and come back. Otherwise you can apply the above method, but you need to look here:
SAVEGAME_PARTYLIST\SAVEGAME_PARTYPOOLMEMBERS
You will see some numeric sub branches, each represents a companion character, open each and look at the topmost value called TEMPLATERESREF and you will see the character's name in the string value. One you have located the correct character, open the SAVEGAME_EFFECT_LIST branch and follow the same steps above.
Hope this ends a few headaches and saves a few campaigns for people.
I'm working on a simpler method (I hope) to create a module with a new item which when equipped applies all negative effects to the player or character it is equipped to, this should hopefully override the existing effects and upon removing the item, all negative effects should go with it. Don't hold your breath though, I'm banging my head against my lack of scripting know-how and lack of examples and documentation.
I find that this option isnt really an option at all for me because i cannot get the toolset to work, i keep getting some error when it's installing. It installs fine, but then it says something about not being able to find the database or something like that. I believe it was an issue with SQL not being able to do something with the file/folder.
Edit: Nvm figured out why it wasnt installing properly.
[Edited by robgw3, 8/30/2010 5:06:55 AM]