Netstat -s showing (and growing) "packets pruned from receive queue" and "packets collapsed in receive queue"
Judging from the information you have provided, and since you seem to have already increased buffers, the problem most likely lies at your application. The fundamental problem here is that even though the OS receives the network packets, they are not processed fast enough and hence fill up the queue.
This does not necessarily mean that the application is too slow by itself, it's also possible that it doesn't get enough CPU time because of too many other processes running on that machine.
Actually, you haven't necessarily increased the buffers; merely the maximum possible size of the queues.
When you open a socket, the queues are set to the value of: net.core.rmem_default = 212992 net.core.wmem_default = 212992
So increasing the maxima will do nothing unless the application is calling setsockopt() to increase the queue size (and failing, if the maximum is below the size it's trying to allocate).
Try increasing the values above.