I can't explain the behavior of the crews servicing your neighborhood. My guess is they don't have clear direction on what to do if people put out mixed glass / metal / plastic in bags - to pick it up, or leave it.

I've been putting out my own recycling in JC since 2007 and the rule in that time has been to put it out loose, not bagged... never had a problem.

As for the reason behind the loose vs. bagged rule: I've read that the sorting machines in some recycling plants get gummed up by plastic bags. No idea what the deal is at the plant JC uses... it might create an extra step to un-bag the stuff, hence the rule / ask.