A number of techniques have recently been developed which aim to increase the performance of transport and application layer protocols when used over links that exhibit high bit error rates and large propagation delays. However, many of these techniques become useless when a network layer security protocol is used, due to the network payload being protected from observation and/or manipulation. The Multilayer IP Security (ML-IPsec) protocol has been proposed as a way to overcome this problem, allowing performance enhancing technologies to be used whilst providing network layer security. ML-IPsec has a number of problems that reduce its effectiveness and cause configuration complexities. This paper identifies these problems and proposes modifications to ML-IPsec, aiming to rectify the issues, whilst embracing the key features and benefits of this multilayer security protocol.