This is a result of a fee such as shipping being included in the eStore. When the transaction is processed into The Raiser's Edge, only the amount that was paid for the items themselves will be put into the store. Additional fees such as shipping will be excluded.

For example:
A user buys a book for $10. Shipping on the book is $4.50.
The user pays $14.50.
Merchant services will show $14.50.
The Raiser's Edge will show $10.