Scholarship Information
Your best bet would be to make contact with the scholarship people and ask (nicely) for feedback as to why you did not get a scholarship. This way, you'll know for certain as to why they did not award you a scholarship. 

Often, scholarships are not just based on GPA/GRE scores or any other academic performance, there are often a myriad of other criteria they use to assess an applicant's scholarship suitability.  Did you have to fill out a form with some details or supply a personal statement?

How do you know that they 


  just took their time to file it.


If they did (which I doubt), then yes, it could be a factor, but I doubt a malicious one considering the amount of information that they would have to file, collate from the many applicants.  More likely, they filed your additional transcripts as soon as they received it (or very soon after).