Hi
I solved the issue by doing the below steps.
First copied my original version web folders in to www\root.
Then imported mysql backup and made my 1.9. version working environment in windows just as in linux.
Then downloaded the newer version 1.15 and overwritten the files from upload to www\root
Refreshed the Login page which asked for upgrade and it all went through successfully.
The mistake i did earlier was, first i copied the 1.15 files directly in windows and set up the new blank database while configuring the ticketing server. This caused the db with new fields / table names which was not there in my old db backup. So while upgarding it all shooted with errors as already exists and all sorts of conflicts.
Anyone who is migrating to new version with new server, first replicate your old environment in the new server with web and db as it is and confirm its working. Then just run the upgarder after overwriting the new version files in web root.
Hope this helps anyone.
@ntozier - thanks for all your guidance.. it helped a lot in finding the right directions.