ppslim,
i tried with 4 bots, 1 hub bot and 3 leaf bots, i did as you said and added flags back one by one waiting a little to see if anything went wrong, i didnt see anything go wrong, and as usual they lost flags, channel and global, so i set the "private-global" to "mn" (removed "o") which sorted the global +o being lost, but i noticed that one of the leaf bots had a global +o, yet when it joined a channel it wasnt being oped. i killed them all and started with an older version 1.6.10 (even though i had this problem on and off back then) and the same thing happened again.
the only thing ive had loaded diferent from when i was on 1.6.8 to now is slenox's netbots scripts, and somehow i dont think its due to those(maybe, but i doubt it)
the only thing i know is, when the leaf bots connect to the hub and download the user file they lose certian peoples channel flags.
also, going back to the problem i had with bans not being shared, if i have 2 bots on one channel, and i ban someone, after a certian ammount of time the bot that didnt place the ban removes it and then the bot that did puts it back, and on the party line of the bot that removed it, all you see is "Channel ban *!*@lame.org on #channel rejected - channel not shared." yet the channels are all set to "+shared" in the .conf files
anyway, i hope i get this sorted, its getting too much hard work on my fingers readding all them flags back.