We started a new server, all stock, running on v0.2.4.1. We have a consistent problem of reverted or recovered spacecraft staying around for other players. When I connect to an empty server, there will be some craft on the launch pad, some splashed down still sitting there and so on. I sort of feel the problem has been around for a long time, are we doing something wrong?

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Please upload your server log file to a service like Pastebin and link it here.

Sorry for the delay, here are two consequent days of logs:
http://pastebin.com/6rWRC7v8

The logs couldn't help much (was hoping to find some error or anything related to vessel recovery), so you could try running dekessler or the nukeksc commands. Read their help text first before executing them.

Will do, thanks!