Code:
	i=0;
	a=0;
	while(pass[i]!='\0')
	{
		if (pass[i]==cleared[i])
		{
			i++;
		}
		else
		{
			a=1;
			i++;
		}
	}
Is strcmp() not working ,then?
I think you might have a stray '\n' character in your input file.

If you wish,
Code:
		if (crypted[i]==99)
		{
			crypted[i] =122;
			cleared[i] = crypted[i] ;
			i++;
		}
		
		if (crypted[i]==98)
		{
			crypted[i] =121;
			cleared[i] = crypted[i] ;
			i++;
		}
		if (crypted[i]==97)
		{
			crypted[i] =120;
			cleared[i] = crypted[i] ;
			i++;
		}
could be replaced with
Code:
        if(crypted[i]<=99 && crypted[i]>=97){
                cleared[i]=120+(crypted[i]%97);
        }
	else{
	        cleared[i] = crypted[i] - shift;
        }
        i++;