I just set up a fresh brand new v1.3.7.1 install and tested echeck transactions using the IPN module with PDT enabled.

All my transactions (large amounts and small amounts, lots of products and only single products on the order, downloads and non-downloads) tested fine. Orders paid by echeck were inserted into the Admin immediately, in Pending status.
Once marking the payment as 'cleared' (testing in sandbox allows control over this), the order was upgraded to "Processing" automatically. All the details show in the customer order history as expected.

I can't see anything specifically wrong with echeck support using the IPN module.