When I first joined Protagonize, I posted a story "In the Teeth of Darkness". I posted three chapters before deciding that I wanted to work on it exclusively for possible publication. Luckily, at the time, there were no other cotnribtors.
Having had the first chapter or so in its' original form here might impact the story's publication. But I think it's changed substantially enough that it won't make a difference to the end-product.
Unless you're thinking of working existing Protagonize stories, copyright shouldn''t be an issue. And it's a fine-line about the first publication rights.
If you're talking about your writing in general here, I can't see how it'd have a detrimental impact. This site serves a fantastic purpose--similar to other sites out there, such as the Critters story workshop and others. The publisher won't have and shouldn't ask for the rights to any previous writing, wherever it's published. Going pro doesn't mean going exclusive (unless you sign a contract to that effect).
This site is different from other writing sites because it promotes collaboration, and there's a lot of benefit that can come from learning to work together with other writers. Any agent or publishing house should recognize the value of this.
If you consider going pro, simply start making a point of keeping the ideas you want to work off the site. Instead, submit those ideas that you don't know what to do with or those ideas that you've dead-ended on.