The filters for transaction ID and (more importantly) payment instrument don't have any effect when searching for transactions to add to an accounting batch. Neither the Payment Instrument in the optional constraints when you first create the batch nor the Payment Method filter in the Search Criteria above the list of transactions has any effect.
Tested on both the 4.5 and 4.6 demo sites:
- Go to Contributions > Accounting Batches > New Batch
- Set Payment Instrument to Credit Card and hit Save
- See that there are a bunch of transactions with other payment instruments.
- Edit search criteria to set Payment Method to Credit Card and hit Search
- See that nothing changes.
- Edit search criteria to set the Transaction ID to "12345"
- In 4.6, see that nothing changes. In 4.5, the Transaction ID seems to work.