Thanks Rick for your help.
I want to pop in on this issue to tell everyone that we do have a bug that is often or likely the issue when you have a BI batch that says it is out of balance.
We have bug 16261
Flexible Billings invoice batch numbers and AR batch numbers can overlap and cause issues.
KB 2953578 gives the update for this for 2011 sp1.
Change from this bug:
Billings Setup (BI.SET.00) now contains a new field "Last Invoice Register Batch#". The field may be used to change the Flexible Billings AR batch numbers so they do not overlap with batches created in Accounts Receivable.
But, if you don't know to make the batches so that they don't overlap, you can still run into this issue. Documents that are already released in AR batch number 123456 get included with BI batch 123456 and visa versa. Batch out of balance is the usual message but that may be at release time rather than at posting time.
This is fixed in ver 2015 via bug 25080. Per the change noted:
The Billings Setup screen now defaults the "Last Invoice Register Batch#" field to "000000" for new databases. The Invoice & Adjustment Posting screen creates an Accounts Receivable (AR) Batch alongside the Flexible Billings (BI) batch that it had made previously. The BI ARDoc can no longer be incorrectly retrieved with a selection of ARDoc’s from an AR Batch.
Programs changed.
BISET00.exe, BIREG00.exe
So there will no longer be an issue in 2015 (which is now in beta) regardless of batch number overlap.