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Jaguar, I have opened and re-saved all decks and they are fine. Also they don't interact as they should with Captain Sisay: it is another proof that something is wrong.
Here is an attached file, using Lovisa in EDH in a fresh deck, with latest version installed.

PS: Sisay looks unable to tutor also some non-creature legendary spells, as lands: I've seen that nothing happens when selecting Pendelhaven and other lands from Legends set.

Please provide a decklist so we can test it.

Aswan jaguar wrote:Nezumi Shortfang flip card " Stabwhisker the Odious "is missing from the ct_all.csv.

That's because Nezumi Shortfang originally worked using a single slot in Manalink 2.0.
With new slots available the flip cards are now set up with slots for their flipped face in the Manalink.xls - so they can now be coded to act like the 'transform' cards, which they functionally resemble.
Just have to wait till Gargaroz gets round to coding them.

Ok, I've re-tested all legends and now only Lovisa and Lin Sivvi are not working. In fact, Lovisa was already recognized as buggish. Now, since there may be other cards that are missing the legendary attribute and obviously both Karakas and Capitain Sisay are buggish as well, please restore this thread among bugs, so that players may report here the legendary creatures that are misworking.

I checked and made decks and played with the first 3 creatures you posted EDH games,that's why I tagged it as not a bug,it is an illegal card most probably in the deck.
Now,that I thing of it I had some problems with decks in EDH that wasn't changed by the in deck ediotor.Try this:
1)In Manalink configuration settings set Read by name=1,
2)then load your deck and make sure there is not an illegal card in it,
3)then save the deck,if everything is fine then,
4)test your deck EDH.

Sometimes also it helps if you close magic and reopen it.

It was already done: I have updated all of my decks in that way.
I've made a test with 95 plains and 4 benalish hero (or mountains and 4 lightning bolts) and the result is the same. Those creatures (Lovisa and Liv Sivvi) are marked as invalid because they miss the code for the legendary attribute. Most likley, there are other cards like that.

Ok, confirmed Lovisa Coldeyes was working for me as I already had the correct value set in one of my magic files.
Both cards miss the correct value in ct_all.scv

I've updated the contents of my first post: please, restore it among the bugs. I think it would be very comfortable for Gargaroz to see which cards are missing the legendary attribute.

Describe the Bug:
Whispering Specter when chosen to sac to discard,discards but doesn't get sacrificed.

Which card did behave improperly ?
Whispering Specter

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
Manalink 3.0

What exactly should be the correct behavior/interaction ?
Whispering Specter when chosen to sac to discard must get sacrificed.

Are any other cards possibly affected by this bug ?

confirmed

Describe the Bug:
Goblin Offensive can't be cast,asks wrongly to pay RR instead of X1RR and when you pay RR nothing happens.

Which card did behave improperly ?
Goblin Offensive

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
Manalink3.0,duel

What exactly should be the correct behavior/interaction ?
pay 1RR to cast it and then X.

Are any other cards possibly affected by this bug ?
-

confirmed

Describe the Bug:
Time Bomb does not get time counters put on it during your upkeep.

Which card did behave improperly ?
Time Bomb

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
28 January 2012 : Manalink 3.0 - Duel

What exactly should be the correct behavior/interaction ?
See above.

Are any other cards possibly affected by this bug ?
No idea.

Describe the Bug:
Gilder Bairn's activated ability has the wrong cost, it's , while it should be .

Which card did behave improperly ?
Gilder Bairn

Which update are you using?(date,name)Which type(Duel,Gauntlet,Sealed Deck)
28 January 2012 : Manalink 3.0 - Duel

What exactly should be the correct behavior/interaction ?
See above.

Are any other cards possibly affected by this bug ?
I don't think so.

Fixed.