I've just stumbled upon the Snowflake Pro software and have been very happy with how it has improved the quality and completeness of my manuscript. At the end of the process, the software uses all the information you've entered to put together a draft proposal to take to editors and agents (after being polished up of course), but being new to the scene I don't know if such people take something seriously if it was composed in part by a piece of software. For example, I know some people interviewing job candidates will throw out resumes if they spot evidence that it was written in part by a consultant or if it uses a typical template, or will in other cases use it as a strike against the candidate even if they call them for an interview. I truly think Snowflake is a great tool and doesn't compromise my work in any way, but I'm wary of others being prejudiced against it for whatever reason. Has anyone encountered this prejudice before?
It would be hard to answer this question without being an agent or an editor. I'm sure each individual agent, editor, and publisher has his or her own criteria in evaluating a manuscript and considering either taking on the writer as a client or publishing the manuscript. Regardless of the individual's personal criteria or preferences, the one common thread that you can expect from each of them is the desire to have a good, solid story.
Frankly, I don't think anyone would care whether or not you used this software to help develop your story any more than they would care whether you used Microsoft Word or Google Docs to type it up and prepare it. For them, the ultimate deciding factor is the quality of the story and the writing. I don't see any reason to even tell them that you used any particular software product to help you develop and create your story.
Having said that, however, the burden of responsibility falls on you to ensure that the finished product is of a sufficent quality before you attempt to present it to anyone for consideration. That means making sure that any residual comments, instructions, or other incidental content that is created by the software has been removed. The bottom line is to make sure that your work is the best you can make it.