Ditto for INV_HIST_HDR and probably some others. I'm pretty sure they used to default to a logical sort, but believe it got broken in the July update.
 
Not sure why the default sort is by CUSTOMER when you're only looking at shipments for A customer...

When you are calling a grid from a program (such as AR-A calling the Invoice Headers) we have to use the primary sort as Customer because we need to quickly index on only the invoices belonging to that customer.  Similarly, IN-A has to use Item Number as the primary sort.  If there is not a compound (secondary) index used then the records will then be in natural order which is normally chronological order.  However, when update has to rebuild a file, the natural order gets scrambled and the entries appear random.  From the FAQ page on the website:
 
When files get out of order by updating or reindexing, we used to be able to use the Pervasive Rebuild and specify the appropriate key and rebuild them in the desired order. However, with the newer releases of Pervasive, it does not work. This is because of certain parameters embedded in the GUI interface for the Rebuild program that you are not able to change. There is, however a command line version of the rebuild that will allow the parameters to be specified.
 
At a command prompt (and the program is located in the PVSW\BIN folder which is in the environment path so you do not need to specify the path to the RBLDCLI.EXE)
 
RBLDCLI -m0 -k0 D:\DBAMFG\DEFAULT\BKARHINV.B
 
The first parameter is always -m0 and the second is -k{Key Number}
 
D:\DBAMFG\DEFAULT\BKARHINV.B is the path and file to be rebuilt. You can use wild cards in the filename to rebuild multiple files.
 
Thanks to Bill at Goldstar Software
 
Some common files and key numbers are:
 
Data that is out of order          File              Key
 
Shipments in AR-A or CM-A   BKARHINV         0
Open Sales Orders in AR-A    BKARINV           1
Shipments in IN-A                BKARHIVL          0
Open Sales Orders in IN-A    BKARINVL          0
PO Receipts in IN-A              BKAPHPOL          6
Open PO in IN-A                  BKAPPOL            0
Work Orders in IN-A            WORKORD          1
Transactions in IN-A             INVTXN              3

Before running the rebuild command, we should backup those files and get everyone out of the system, right?

I'm not sure if this is related or not, but we are seeing some significant delays when looking up inventory items, then clicking the SO icon to view Sales orders. If we rebuild the files per above, will it help this respond quicker?