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 at this time).
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...
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.
You can make spotting the effect much easier by removing ALL equipment from your character and then re-saving. This may even cut the number of branches you have to check to just the one with the negative effect
For those who saved after using the trainer option to try and remove the effect, you may have a problem spotting the offending effect now 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.
Also, after removing the effect/s, check your characters stat's after the effects are gone and before you re-equip your gear and weapons. Check to make sure that your resistances, attack, defence and armour values look normal. If any of them are negative or unusually high, you may have some left over issues that need fixing. To sort this you can create a new game and character using the same race and background as the character you're trying to repair, then using the trainer add experience points and level the new character to match. Fill-out the skill and talent trees the same and insure attributes are likewise. Once all that's done (don't forget to account for stat bonuses from class specialisations) note down the new characters stats and compare them, make a note of which ones need fixing and then go take a look at this page:Link
That should have all the info you need to correct your character.
If you want to remove an effect or stat issue 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:
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 you find this useful.