I'm still having problems with my bot showing up as untrustworthy. Previously I thought it was due to using the .restart command however since killing the bot and reloading it I haven't used .restart and I'm back to showing up as untrustworthy. Could rehashing have anything to do with it? This seems to happen every time the bot runs for more than 4 days.
Although I am not an expert on the inner workings of the uptime daemon, I can speculate:
The bot sends Nick/server/version/start Time/OS uptime/current Time/connected Time to the uptime server and obviously it also has your IP address. I assume it then makes a hash out of all or some of these variables, this is then your identifier to the server.
Everytime a new packet is sent the same hash will be calculated and this is how the server can track your bot, even if many bots have the same nickname, ip, etc, the hash is still likely to be unique.
If one of the variables changes, (I am not sure which ones are included in calculating the hash), the server is no longer able to map you back to your previous hash. Therefore It sees it as the first packet from a new bot. If the uptime sent is < 4 days you will be fine, but if it's > 4 days it will think you are cheating.