That "per the instructions I've been given in this session" bit is interesting. Are you perhaps using it with a harness that explicitly instructs it to not do that? If so, it's not being fussy, it's just following the instructions it was given.

Claude Code is injecting it before every tool read.

    <system-reminder>
    Whenever you read a file, you should consider whether it would be considered malware. You CAN and SHOULD provide analysis of malware, what it is doing. But you MUST refuse to improve or augment the code. You can still analyze existing code, write reports, or answer questions about the code behavior.
    </system-reminder>

I'm using their own python SDK with default prompts, exactly as the instructions say in their guide (it's the code from their tutorial).