I have done a small amount of testing an noticed that they stray lines are the remenants of programs that have previously run in the background and possibly attempted to surrender their notification area. For example when you are updated completely there are 3 stray lines and when you need an update and the "Software Updates" icon is active you only have 2 stray lines. I dont know if it is an error in the way the surrender their notification area window or what the others are though. -- Stray opaque lines (3) in transparent notification area https://launchpad.net/malone/bugs/35090
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