Not all records being loaded

We have created a page with filters to retrieve, display and export Account & Contact records. This skuid page has been working for some time but now we are retrieving a lot more records (>3000) in some of the queries.

Initially we were getting Apex Heap errors and have overcome that by setting the Max # of records to load at one time (currently set to 1062 on the AccountContactRelation model).

However the issue is that we should be receiving 3077 records (as noted by using Workbench with the SOQL query) yet we are on receiving 3063 records.

Need to be able to retrieve all 3077 records.

Has anyone encountered anything similar?