Hi Adam,
Per
this KB article, Marketo looks at the SystemModStamp on the Salesforce record to know if it has been modified since the last sync with Marketo. If it has, then it will sync the data updates back to Marketo.
Everytime the Marketo Sync connects to Salesforce it will scan records and look at the "SytemModStamp" (salesforce system field) for each one of them. It will compare this value with the stored value, which was pulled at the last scheduled sync. If the values match, Marketo will move on to the next record. If the values are different (new value later date than previous value), then Marketo will do a compare and contrast of all fields on that record in both systems and update the information as needed.
Can you verify that the Integration which updates your data every night is modifying the SystemModStamp? You will know if it isn't if the record's Last Modified Date and Last Modified By is not the Integration user from last night...
-Kyle