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I am dealing with an update of an application and we have some code inside that is using the "Propel::addMultipleJoin()" method. I know it is marked as deprecated but we are using it and it is still in there.
So we are creating a "Criteria" object and using the "addMultipleJoin". The "addMultipleJoin" method itself calls the "addJoinObject" which is calling the "equals" method of the join object (class "Join") for each already added join object. Now things starting to differ between the versions.

Version 1.7.x

The "addJoinObject" method is the following:

public function addJoinObject(Join $join)
{
    $isAlreadyAdded = false;
    foreach ($this->joins as $alreadyAddedJoin) {
        if ($join->equals($alreadyAddedJoin)) {
            $isAlreadyAdded = true;
            break;
        }
    }

    if (!$isAlreadyAdded) {
        $this->joins[] = $join;
    }

    return $this;
}

The "equals" method itself is checking the following criterias:

return $join !== null
    && $join instanceof Join
    && $this->getJoinType() == $join->getJoinType()
    && $this->getConditions() == $join->getConditions();

What have I done to debug this? I simple added the following code in "Join::equals()" right before the return statement and added a breakpoint to get the content out of it.

$joinParams = array();
$joinAsArray = array(
    'clauses' => $join->getClause($joinParams),
    'conditions' => $join->getConditions(),
    'join condition' => $join->getJoinCondition(),
    'join type' => $join->getJoinType(),
    'operators' => $join->getOperators(),
    'params' => $joinParams
);
$thisParams = array();
$thisJoinAsArray = array(
    'clauses' => $this->getClause($thisParams),
    'conditions' => $this->getConditions(),
    'join condition' => $this->getJoinCondition(),
    'join type' => $this->getJoinType(),
    'operators' => $this->getOperators(),
    'params' => $thisParams
);

Version 1.6.9

The "addJoinObject" method is the following:

public function addJoinObject(Join $join)
{
    if (!in_array($join, $this->joins)) { // compare equality, NOT identity
        $this->joins[] = $join;
    }

    return $this;
}

For your information, the class "Join" implements the magic "__toString()" method. Thats the fact why the "!in_array($join, $this->join)" is working.

public function toString()
{
    $params = array();

    return $this->getClause($params);
}

public function __toString()
{
    return $this->toString();
}

As you can see, in 1.6.9, the clauses where the base to validate if the join was already added or not. In 1.7.x, the condition (array) and the join type (e.g. "left join") are the base to validate if the join is already added or not. The problem with my statements is, that condition is always an empty array(), the join type is the same so they a marked as equal.

I digged through the changelog and each commit. Two are left, 93c6a0f and dcace44. I found a comment that is discussing this problem. So lets see. Funny sidenote, arvenil introduced this by fixing a bug (and i'm totally on his side, as long as code is inside, bugs should be fixed).

How to deal with that problem while no fix is available?
Currently, i made good process by doing the following replacement.

//broken code
$criteria->addMultipleJoin(
    array(
        array(
            MyTablePeer::COLUMN_ONE, MyOtherTable::COLUMN_TWO, Criteria::EQUAL
        ),
        array(
            MyTablePeer::COLUMN_TWO, 3, Criteria::EQUAL
        )
    ),
    Criteria::INNER_JOIN
);
//new code
$criteria->addJoin(MyTablePeer::COLUMN_ONE, MyOtherTable::COLUMN_TWO, Criteria::INNER_JOIN);
$criteria->add(MyTablePeer::COLUMN_TWO, 3, Criteria::EQUAL);

Taking the created sql statement and checking them via "EXPLAIN" is returning the same result and speed.

Update 2014-03-31

I did a pull request which got merged. Let's see if it passes the quality test and will be in the next release.