You're definitely encountering an issue that shows up only when using an older version of CheckBook on Mountain Lion, the latest operating system. We fixed that compatibility issue back in April when we released version 2.3.2, so you'll definitely want to update your copy of CheckBook now that you're on the new OS. To do that, choose 'Check for Updates…' from the CheckBook menu at the top of the screen. Or, if you purchased from the Mac App Store, check for the update in the Updates section there.
Once that's all installed, you'll be able to change any submitted zero Amounts to the correct value and they should stick.
_________________ Allan WoodallPhosphorescent PhageSplasm Software http://www.splasm.com
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