I’m having the same problem. The current Custom GPTs (new GPT-4o) ignore the system prompt (Instructions). In the first response of a session, GPT ignores even basic instructions written in the system prompt and follows the user prompt instead. I think this is an issue with OpenAI’s internal settings.
OpenAI has been neglecting many of the problems happening with GPTs. I’ve been using GPTs since their release, and I’m very disappointed with how OpenAI is handling them.
As a temporary workaround, you can repeatedly tell GPT to reread the system prompt during the conversation. This might improve its responses afterward. Give it a try.