Hi Sai,
How many CPU cores do you have on your VPS?
Just to calibrate expectations, we're not going to be able to tell you why a second install is acting differently. Assuming the software is the same (we've have not made any changes to the BigBlueButton server over the past few months, only to the client to support later versions of Java for desktop sharing), you should have the same experience.
That also does not make sense as the video packets are simply passed through the server -- there is no transcoding, just a pass through.
Recommend you look at the various CPU monitoring tools that are available for Linux and try to narrow down what processes are taking CPU.
Also, we don't recommend running BigBlueButton on a VPS as FreeSWITCH, the software switch that handles the conference, requires a hardware timer to handle the incoming audio packets. Without a hardware timer, FreeSWITCH must work harder (more CPU) to handle the incoming packets in real-time.
Regards,.. Fred