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that's how it worked for me, once I fixed the glitch. although, the pirate invasion bar, music and enemies would randomly switch to that of the windy day event, which was at the same time I was looting the pirates. I think that is the issue, overlapping events
so, what happened for me is that I begun the fight with skeletron, and realised that my gear was doing nothing to it on master difficulty (was trying to get the relics), so i set time to day to get it to leave. apparently changeing time to day made skeletron start spazzing on top of me like he...
I had a similar problem, I believe it is to do with the windy day event, as that was messing with the pirates for me.(the event took waaaaay too long to start, and would temporarily end for no reason.)