Recently, Joint Source-Channel Decoding (JSCD) techniques have been proposed to improve the reception of multimedia contents transmitted over error-prone channels. These techniques take advantage of the redundancy left by the source coder and of bit reliability measures (soft information) provided by channel decoders to correct transmission errors. To be put at work, protocol stacks have to be made permeable to transmission errors in order to allow soft information to reach the upper protocol layers. For that purpose, headers have to be reliably estimated at each protocol layer. First results have been obtained for lower protocol layers (PHY and MAC) protected by CRCs. The aim of this paper is to extend these results to upper protocol layers (IP and UDP-lite) protected by checksums. As for CRCs, trellis-based decoding techniques may be employed for data protected by checksums. Nevertheless, specific tools have been proposed in this paper to reach a complexity-efficiency trade-off.