Huene, that's not a problem with GregTech or NEI, it's a config file mismatch between client and server.
There can be mismatches if the server is running the very first release but the client updated. And since clients update automatically and servers don't, you can pretty much expect this to happen on any "first hour" server. Basically, the clients got an updated config that the server doesn't have, but the server has the final say about recipes. So even though the client sees the recipes in NEI that are valid for its version, the server says "no, my config is different, you're not allowed to craft that".
This has already been fixed for quite a while. Please ask your server admin to copy a GregTech config file from an updated client to the server directory.