What field are you using on the Account spreadsheet to identify the Primary Contact? If you are using full name and there is more than one Contact record with that name (eg John Smith) then CRM won't be able to decide which one you mean. Use something more unique such as email address, then in the mapping for the Account records, configure the Primary Contact lookup field to use the email of the Contact as the key, rather than the name. Alternatively, add a field on Contact to import a unique ID (for example based on date + row number like 201604260001) and use that to key them together.
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