Will different signatures in academic mark sheets cause rejection in document verification?

If all other details are tallying they may not worry much for the signature. Generally, over a period of time some changes may come in our hand writing and signature also. There may be minor changes over a period of time. They will verify your signature in the application and may compare with a signature you may do before them.
If there are any other differences, then there will be a problem. Please compare all the certificates for your name, Date of Birth, father's name and mother's name and if they are all tallying you need not worry.
If somebody asks about the difference in signature you can explain them how, why and when the change in the signature took place.
That will not be a hindrance for you to get a job. But now you don't change the signature again and see that the same signature will be maintained for ever.

This does not seem to be a big problem as signatures of an individual from time to time can differ and if same is asked to you, it can be explained.

One thing which I am not able to comprehend is how the signature in 12th certificate in your copy can be different from the online one. Is it that they were done at different times - what I mean is the copy which was uploaded online was signed at a different time and the one which is with you was signed at a different time. And due to casualness the signatures were different.

If it is so then it might create a problem and if the verifying authority insist you might have to get an affidavit for confirming that inadvertent change.

The procedure for affidavit is a simple one and can be done through a lawyer who will make a document where you can take oath and give the details of this mismatch and sign it in presence of magistrate in the court. Once the magistrate countersigns it, the affidavit is ready.

Please take care in future not to change your signatures at random.