I respect you, but here's what:
I don't have any idea what you've got in your database: you do. You've got to run code to figure things out, not me.
Next: I seriously doubt that this code does what you say. Maybe I'm wrong, but let me work through my 'there's a typo' logic:
if($var == 'SCN') \ you say this returns false.
$newVar = $var[0].$var[2].$var[4];
\suggests that you are taking every other character, of $var, yes?
if($var == 'SCN')
evaluates as true
\ don't you mean if ($newVar=='SCN') evaluates as true?
if, after the act of creating $newVar, $var has NOW CHANGED to =='SCN', then I am very bewildeered.
However, if in fact $newVar=='SCN', then you're on the right track to analyzing your problem. MySQL has messed around with the string to store it in BLOB form, probably by padding the stored data with empty bytes.
WHY are you storing a string as a blob in the first place? Storing a string as varchar or text seems much simpler and more to the point. I can't think of many reasons why storing a string as a blob is to your advantage, particularly if you are trying to extract data from the blob.