which is responsible for some batch operations with an SQL table

Is this a native IRIS SQL Table and have you examined the Query plan for the SQL Table?

If you run the report via the browser 

MSDS.Maintenance.Report.CBMReport.cls?LocID=loc&WOID=wo&LineID=lineId&$MODE=PDF&$LOG=1

where the values of loc,wo, and lineId

is there anything helpful reporting in the log.

Might you be able to share the 2 sql statements and the query plans?

If you are running the queries in the System Management Portal there is a limit that you could set 

but I dont imagine that is the issue.

Where possible a COUNT(*) query could chose to use your indices and in theory your indices might be different from your table data but that would be highly suspicios under normal circumstances as the writing to the table and the indices are in a database transaction so it should have all been written or not.  

To your specific question

Is there something inherent with the queries that limits the result set size, or anything I can do to make sure I'm getting back all the results? Rather, than trying to run it about 100 times limiting all previously gotten accounts.

Again if you are running via the System Management Portal there are times I run the query with a limit of 100 for example and once the results are presented I select the Print hyperlink to run the entire query results to a file