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Activity in the Windows system tray (new icons, possibly changed icons) can cause the pointer to become spuriously unhidden when `Hide mouse pointer when typing in a window' is checked.
We've had one report of this on Win2K (5.00.2195). I (JTN) can reliably reproduce it at work with Win2K by sending myself mail (Outlook adds an icon to the system tray when this happens).
Update, 2004-Jul-25: I was unable to reproduce the system
tray behaviour on a Win98SE system, but activity in other windows
messages to be sent when nothing had actually changed. As of tomorrow's
snapshot, PuTTY will ignore such messages. Hopefully this will solve
the original problem; if it works for you it'd be nice if you could
(Aside: the mouse pointer occasionally seems to get shown on my Win98SE
system - as a pointer, not an I-beam - and then isn't hidden by
subsequent typing. I think it may momentarily be an hourglass first.
It's sometimes caused by playing a
.WAV file for a bell,
and sometimes happens for no apparent reason. This doesn't appear to
be visible to the usual PuTTY show/hide pointer mechanisms
show_mouseptr()), so isn't fixed by the above change.)