It's quite hard to answer a MKT Channell question because there are many things that might be causing the issue. What I would do if I was you is checking the marketing channel processing rule and the bucketing position of the two channels. Also, I would check if I'm using an eVar in these two channels (referral or SEO) and the expire after condition of the eVar. I already saw in some cases that users were using an eVar in MKT channels with the expiration of 30 days and it was messing with the processing rule of the marketing channel. If you're using eVar on MKT Channel processing rule remember that MKT Channel works on hit level.
If you can't find an answer, I would recommend contacting the Adobe team.