@alanniergarth - apparently we have seen something similar in the past. I'm not sure if this is exactly what you faced or not but our solution was as follows (if you don't feel comfortable doing this steps, feel free to give me a call or email):
Steps VIA SQL Mgmt Studio:
1. Get all users out of CRM.
2. Backup DB.
3. Disable all Triggers on emaillink table
4. update EmailLink
set eLink_SyncedWithMAS90 ='1' where elink_syncedwithmas90!='1'
5. Enable all triggers on emaillink table EXCEPT emaillink_instUPD
6. Disable all Triggers on phonelink table
7. update PhoneLink
set PLink_SyncedWithMAS90 ='1'
where PLink_SyncedWithMAS90 <> '1'
8. Enable all triggers on emaillink table EXCEPT phonelink_instUPD
Extra Notes per MS:
All records should have values of _syncedwithmas90=1 (even if the record does not have a relationship to mas)
0 values are records that were not synced for some reason due to a power outage/system failure/service failure/etc. (if anything...a small number)