Paya finally got back to me that this is happening only with Purchase Card batches and they will NOT be fixing the issue. The batch totals will just display incorrectly.

The only resolution is to export the batch to Excel and sum up the totals manually.

We had this problem as well.   Whoever you spoke with at PAYA was incorrect.  This is the info we got right off of their website and how here is how to find it.    I hope this helps. 

Problem: PAYA is not displaying all transactions under a settled batch report.
Log in to PAYA
Click on HELP (upper right)
Under the Self Support section, in the Search field, type in “displaying all transactions under a settled batch” click on spyglass.

This will take you to another screen “Looking for Something?” Type in your search criteria again.

When the search results come up you will see your topic. Click on the result (top one)
This is their “fix”.

Displaying all transactions under a 'Settled Batch Report' in Paya Exchange

Product: Sage Exchange 

Description:

There are times when a sub-user does not see all transactions within a particular settled batch. This is mostly due to a limit placed on the ‘Devices’ portion of the role the user is associated with. The Admin, or at least a user with administrative prerogatives, can help remove these limitations. For the purpose of this article, we will assume ‘Joe Smith’ is a sub-user, and his role type is ‘Settlement’.

Resolution:

Upon logging into www.sageexchange.com (aka PEMS), the admin would navigate to the ‘Administration’ tab, and click on ‘Roles’. Locate the role you would like to amend (since we already know both the user and the associated role), we would simply locate the role and click on ‘Edit’ beside it. Under the ‘Role Edit’ page, scroll down to the bottom, and make sure that the ‘Select All’ label is checked beside 'Devices'. This will ensure that every settled batch report would show all of the transactions that it contained at the time of settlement.

We never changed anything and suddenly it just started to work correctly.