Plugins.pl has nothing to do with your problem.
What version/Date of source were you previously running and which one are you using now? Are you seeing a lot of chat messages in game? If you have a lot of logging turned on, I have found that it tends to start queuing up and #commands aren't very responsive or won't work at all if you are getting spammed too much.
I haven't seen any issues with #repop or zoning other than when I had turned on perl debug logging and was using a massive loop that was sending non-stop quest::debug() messages to my chat window.
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