Fortunately, your message is not clear. Can you please elaborate what do you mean by "but when it does a check it still does A LOT of checks in a cluster, then stops". From your post, I understand your query regarding health check issue has been resolved. Please let me know if I misunderstood or you still have some further questions?
Regarding LB session affinity issue, Did you find anything in suggested stack driver logs for the back-end services and Cloud Load Balancer? Have you checked and verified all suggested causes(Backend instance capacity, health check failure, Auto-scaling adding/removing instance etc. ) for losing affinity session?