>
>
> If you have DISH Network receivers, the following pages will help:
>
> http://www.mythtv.org/wiki/DISHNetworkLIRCConfiguration
> http://losdos.dyndns.org:8080/public/mythtv-info/MythTV_DISH_IR_LED_TX_via_Modified_LIRC.html#Note_for_MultiDISH_users
>
> I've never tried it myself. If you don't have DISH, you may have to get a different (or a second) IR receiver/transmitter.
>
> Good luck,
>
> Adrian

Thanks for the tip but I don't have DISH box. It turned out that problem was too simple. The second settop box  was in close proximity to the first box and hence was picking up its signal. Once they were separated things were fine.
I was trying to fix this remotely thus didn't know the boxes were too close. A pair of local eyes helped in sorting it!
Both the ports are now sending signals independently and not simultaneously as before.