hi,
same for us. We fighting with the same problem on our CRS317-1G-16S+ (http://forum.mikrotik.com/t/os-6-43-12-4x-crs317-1g-16s-mstp-problems-between-two-link-up-down/128269/1). We thougth, it might be a configuration issue. I replaced cable, SFP+ modules (Allnet / Ubiquitiy) but nothing helped. Now I replaced the both ports (core-03 and core-04) with the 10G copper SFP ports and its seems now stable.
We replaced in the first time also one switched, which helped (core-lan-01). But now we have the same issue between core-lan-03 and core-lan-04.