I apologize for the delay in response, this question was buried in our system under quite a bit of spam.
You’re not doing anything wrong — this is very common with white pine that’s been weathered. Mold and weather staining often penetrate deeper than sanding can reach, so sanding alone usually won’t remove it evenly. Clear stains actually highlight blotching, which is why it looks worse now. To fix it, you’ll likely need to clean or treat the logs with a wood brightener or stain-blocking prep product, then switch to a lightly pigmented (semi-transparent or toned) stain to even things out. Going forward, keep logs protected from weather before installation and avoid clear stains on pine — they’re unforgiving.