Mysqli prepared statements have a different result than a straight query - php

Question

So, I'm working on some PHP and using prepared statements to access my database with mysqli, the following statement has a different outcome when prepared statements are used than if I
run the query using HeidiSQL, manually inserting the values
run the query without using prepared statements and manually entering the values
Prepared statement query:
$qStr = "SELECT id, head, descrip, img.dir
FROM CS_P, img,Q_Q_Items
WHERE CS_P.id = Q_Q_Items.I_ID
AND CS_P.id = img.Product_ID
AND img.priority=1
AND CS_P.id NOT IN(
SELECT ID2
FROM I_Cols, Q_Q_Items
WHERE ID2 = Q_Q_Items.I_ID
AND Q_Q_Items.Q_ID = ?
AND ID1 IN (".$madeMarks.")
)
AND Q_Q_Items.Q_ID = ?;";
Manually entered query:
SELECT id, head, descrip, img.dir
FROM CS_P, img,Q_Q_Items
WHERE CS_P.id = Q_Q_Items.I_ID
AND CS_P.id = img.Product_ID
AND img.priority=1
AND CS_P.id NOT IN(
SELECT ID2
FROM I_Cols, Q_Q_Items
WHERE ID2 = Q_Q_Items.I_ID
AND Q_Q_Items.Q_ID = 2
AND ID1 IN (35)
)
AND Q_Q_Items.Q_ID = 2;
The difference:
This statement is intended to omit rows where the value of ID_Cols.ID1 matches one of the values to be bound in place of $madeMarks. $mademarks is just a string of question marks that are inserted into the string so that I can insert numeric values that are posted to the PHP using AJAX and correspond to choices the user has previously made.
When I run this query on the SQL server directly it correctly omits rows where ID1 is in the values entered in place of $madeMarks in the prepared statement, with prepared statements these rows are always included and they shouldn't be as this means a previous choice made by the user clashes with this choice meaning it should not be displayed.
Is the way prepared statements are processed making this query impossible to be executed as intended?
Further information:
I have echoed out the values and they are correct integers, no strings or characters and all of the data is correct before it is bound to the prepared statement, I have used intval to make sure of this.
JSON encoded array of values bound to the query:
[2,35,2]
Bind type string:
'iii'
$madeMarks:
'?'
I have bound the values to the statement with 'i' binds as the database is expecting.
ID1 and ID2 are integers.
//////////////////////////////////////////////////////////////////////
It is now functional.
This isn't really an answer but is is a workaround, I just used preg_replace to replace any non-numeric chars with empty characters and then built the in statement with a for loop, inserting values from the choices array into the statement. There is no vulnerability to SQL injection as it is only numeric characters, this would be vulnerable to injection if it was a string that I had to compare.
Do not do this, it is hackish and bad, just use PDO.