When you make a change in ssh Xbian-config (Say updating OC values) you are asked if you want to reboot. Selecting No has the desired effect - however in XBMC you are still prompted if you want to reboot.
There is no need for this - the system should know where the "change" was made (either ssh or XBMC) and only display the reboot command on the appropriate screen.
that is by design.
what about case you login with ssh and your wife is watching tv directly ?
What would be worse... in that scenario is that I am upgrading the system and the popup appears on the TV downstairs and "her indoors" say's "Ok" - Doh.
Not an issue more a point.
the "problem" is not that simple at all. just for start - if you find elegant solution - no problem to implement it.
anyhow from the system perspective this all is happening:
all xbian* packages & xbian-config is following Debian policy with reboot-required semaphore file.
xbian-config has internal function to check for that file. xbian-config-xbmc is solely calling that internal function. the function itself will not return "yes" until apt & dpkg finished - that just means you will not get "reboot" request prior upgrading is done.
the file is commonly used by other system components and also upstream packages are creating it in case they would like to reboot (libs/base tools/kernel/etc).
auto-update subsystem is using that too. so the file & user notification by XBian can by also triggered by non-user actions (so without originator ssh or xbmc). auto-update subsystem has some shutdown tasks which also rely on that semaphore file.
xbmc will ask you only once (if NO is choosen, xbmc will not ask again).
and the most relevant point - this notification is there because REBOOT IS REQUIRED. if libc is updated without services restart or reboot, it's only question of time of random problems / crashes. but the same applies for instance if XBians libcec, libtag, shairport libs would be updated and XBMC won't be restarted (or reboot).
if it is such problem and you want to silently ignore that fact, only proper solution would be a switch yes/no in xbian-config-xbmc at updates controlling the popup dialog within xbmc. so the reboot check will never run in xbmc.