Hi Nikhil,
I too faced the similar issue.If I am not wrong, your application is working on the entitlements where your main URL doesn't change but your referring URL (dynamic) does.
But as a work around, as Harlett suggested, you need to look into your component details which would be differing in one or the other sense.
For e.g., in my case it was a portal WAS server where requests are been entertained at front-tier passing from Webserver. Therefore, we use to get a component called "Portal Description" in Response Headers which actually represents your business transaction. [This is nothing but Portal page name pertaining to each portlet]
Similarly, you can check for Referring URL etc which might be unique to every transaction. So as suggested, please take help of Fiddler (or even recorded sessions will be having those data) to identify unique transaction.
I would suggest perform recording transactions manually and then go with bulk option.
Hope it helps.
Regards,
Vaibhav