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If PuTTY starts up with its window unselected, something slightly odd can happen with the cursor: it doesn't revert from box to block when the window gains focus. JTN, 2003-01-23: Possibly related: I've also noticed that if PuTTY starts up without focus as a result of being run from `wf' (DoIt), on Win2K, it doesn't get a taskbar entry until it received focus (although it's visible on Alt-Tab).
Audit trail for this bug.