Strange Problem with 16 byte packets

Hi, I am using a proprietary protocol and sending a bunch of bytes to a Draytek router at an enterprise site. When i send the data in TCP batches of 1 MB i see no problem. However, when i first send 16 bytes followed by 1 MB of data, and then repeat this till the entire data has beeen sent out. During this process I see that my TCP session times out. Unable to understand why this could be happening? How can sending 16 bytes of data followed by 1MB of data affect the transfer. Thanks !