I also thought Prototype had fixed all of these issues.
This isn't necessarily Prototype's fault. Well it is and it isn't. It is because yes, it extends the behaviors of the elements which resulted in your little collision. But it isn't because it's this type of "sugar" that people who use it are looking for. It's really a good practice to get into anyway, to create namespaces instead of global functions. So unfortunately you ran into it by mistake, but something good came of it, in that you now realize what to do to avoid it in the future, and again, not just in regards to Prototype but any lib you drop in for whatever reason...
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