The only contretemps I've encountered with echecks was my introduction to them. What I did initially was print out the check and instructions and took the entire print out to my bank. The teller was not familiar with them but called the manager over. Manager was familiar and gave the teller the go ahead. No issues since then whether to deposit, cash or edeposit.
There are several echeck issuers. Here are the FAQs from Deluxe.
http://www.deluxe.com/echecks/faq
Please click on the "Using Deluxe eChecks to protect against fraud." Maybe that will reassure you and your bank.
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