Without examples, I’m not really able to advise. There should be no reason for a failure, unless it contains cdata
(see the FAQ). It’s highly likely that the issue is unrelated to this plugin.
When trying it with this plugin, check the page output and see if the script is appearing in the source exactly the same as you pasted it into the custom field on the post. If it does, then the issue is not with the plugin but the script itself.
I hope this helps.