Posted to mongo users group also. Looking through the existing bugs I found
a bug which sounded similar which was that hint() didn't work with count(). There was a vague comment that the results returned when using hint() would not be valid, but nothing more. I'll look up the bug number after this.

I'm attempting to isolate a performance problem with some PHP code and MongoDB.
I'm beginning to think that either hint() or explain() doesn't do what I think it should do.
In the PHP below, I use to not have the hint. It was painfully slow. Putting the
hint in made things quicker, but the results don't seem correct. I'm sure I'm missing
something, but have a read. Thanks. MongoDB version 2.2.1.

I'm doing the following in PHP:
$results = $db->Results->find(array('Test Results' => array('$exists' => true), 'atSchool' => 'yes', 'onNetwork' => 'yes', 'schoolID' => (string)$s['_id']), array('_id' => 1));
$results = $results->hint(array("Test Results" => 1, "atSchool" => 1,
"onNetwork" => 1, "schoolID" => 1));
$numR = 0;
foreach ($results as $r)

{ $numR = $numR + 1; }

or in mongo shell:
db.Results.find( { "Test Results" :

{ "$exists" : true }

, "atSchool" : "yes", "onNetwork" : "yes", "schoolID" : "550627000691" }).hint(

{"Test Results" : 1, "atSchool" : 1, "onNetwork" : 1, "schoolID" : 1}

).explain()

Now here's the issue. explain() returns n=113, which if I read the document correctly should be the number of results returned.
Yet if I run the above mongo shell command with count() instead of explain it returns 5641, which I believe is the correct number.
The PHP code seems to return the same as explain().

explain() output:
{
"cursor" : "BtreeCursor Test Results_1_atSchool_1_onNetwork_1_schoolID_1",
"isMultiKey" : false,
"n" : 113,
"nscannedObjects" : 177,
"nscanned" : 6531,
"nscannedObjectsAllPlans" : 177,
"nscannedAllPlans" : 6531,
"scanAndOrder" : false,
"indexOnly" : false,
"nYields" : 0,
"nChunkSkips" : 0,
"millis" : 50,
"indexBounds" : {
"Test Results" : [
[

{ "$minElement" : 1 }

,

{ "$maxElement" : 1 }

]
],
"atSchool" : [
[
"yes",
"yes"
]
],
"onNetwork" : [
[
"yes",
"yes"
]
],
"schoolID" : [
[
"550627000691",
"550627000691"
]
]
},
"server" : "ip-1-1-1-1:27017"
}

count() output:
> db.Results.find( { "Test Results" :

{ "$exists" : true }

, "atSchool" : "yes", "onNetwork" : "yes", "schoolID" : "550627000691" }).hint(

{"Test Results" : 1, "atSchool" : 1, "onNetwork" : 1, "schoolID" : 1}

).count()
5641

If I check the index I have:
[
{
"v" : 1,
"key" :

{ "Test Results" : 1, "atSchool" : 1, "onNetwork" : 1, "schoolID" : 1 }

,
"ns" : "Edu.Results",
"name" : "Test Results_1_atSchool_1_onNetwork_1_schoolID_1"
}
]

I've rebuilt the indexes, run ensureIndex, etc. No changes. Anyone have ideas?