well, i will tell you the reason. There is a small change in my input data (sorry for that, earlier),so now the ID is completely similar. It used to be similar only after the '.' before. So, i am splitting it with space now. you can try running the program with the input data given below:

SID5141.C1665 SID5141.C2448
SID5141.C1253 SID5141.C2039
SID5141.C1596 SID5144.C1956
SID5141.C1906 SID5144.C2149
SID5142.C1221 SID5144.C1956
SID5144.C2149 SID5141.C2386
SID5141.C2039 SID5142.C1221
SID5141.C5887 SID5141.C7685
SID5141.C1005 SID5142.C2808
SID5141.C1046 SID5141.C1596
SID5141.C2386 SID5141.C4990
SID5141.C7685 SID5141.C4888
[download]

apart from this, i have noted down your other suggestions. i am sure i will improve and take care of all what you have mentioned :)