Ehtesham,
The difference between why one Moodle is playing SCORMs better than the other is explained in the syntax of the hyperlinks. There is a setting in Moodle at Admin > Server > HTTP > Use Slash Arguments. If this box is checked the links to files inside the Moodle course files look like the one in your Moodle 1.9 example. If slash arguments are turned off, the same link has file.php?file= as it does in your Moodle 1.8 example.
So it looks to me like the issue is not which version you are running but how you have the Use Slash Arguments setting configured.
Go in and change the setting on your 1.8 server and see if it works then.
Regards
Rod