IMHO, several conditions will make your Dude implementation stable and reliable.
After running Dude since 1.0 days, I always seem to have a stable system if I stick to several rules and conditions.
1)Run Dude Server on any reasonably powered PC server and I prefer Win2K3 server OS. A 2.8GHz processor with at least 512RAM will always run with headroom to spare. Lesser powered processors could easily work, so just check processor utilization, but more important to see level of network traffic.
2)Definitely run Dude as server process. Installs automatically now and allows start/restart/stop
3)Minimize access to local server Dude interface to just performing backups. It is the only way to get all the XML data exported properly for the backup. Learned that the hard way 
Another ‘backup to the backup’ would be to stop all Dude processes, then zip entire Dude folder. Probably not the best thing to do, but it might save you some day. I used to do it early in new systems as checkpoints. As Dude matured, dont seem to need to do that anymore, but the point is, you can if you want…
4)Develop and access Dude server with client only. This seems to be most stable environment. Accessing Dude through Remote Desktop (RDP) seems to destabilize machine. Suffers from same problem as many other graphical programs. For whatever Windows reason, the video resolution affects display of maps, not just on local machine, but in the client also. In the past has actually caused crashes. WhatsUp has same problem, turns icons all black, cant remember other programs with problems, but if they have graphical interface, many will suffer from similar issues. Word to the wise…
5)Pentium 1GHz to 3Ghz OK. Just have to see what the level of network traffic is. CPU shouldnt be a problem. Depends mainly on polling interval and how many services you are monitoring. Runs very efficiently, but recommend monitoring and noting RAM utilization for Dude processes. If it is running away or ‘pumping’ up to a high level and then back down, something is configured wrong. RAM should stay within a reasonable range, but no way to tell how much it will use. Havent seen any problems recently, but if you do, boot machine, stop all clients and restart everything and it should stabilize. If necessary, roll back to previous backup.
- I dont use routerboards for Dude Servers, or Dude on a PC running RouterOS. Most important problem is that Dude process cannot be controlled like it can in a PC running Windows. Cant stop/restart/start service. Sometimes you just have to stop Dude service, and you might not want to disrupt anything else, so its just not correct platform as main Dude server.
7)However, routerboard running Dude as agent for polling devices far out in network could be very advantageous. That is where I see the most benefit of the Dude package on a routerboard. Dude can be a pretty heavy server process, and like you noticed, you might want to check file sizes, update timestamps, etc. Only possible on PC platform. But when you want to conserve network traffic, this could be very helpful. Just dont load it up too much. You will see how little RAM and
CPU you have left on the routerboard when you let Dude do too much on the routerboard.
Sorry to be so longwinded, but this is how I have run Dude servers that have year-long histories. You will be happy when you see that long history in your graphs, and notice a server has run for hundreds and hundreds of days without interruption.
Hope all these words help 
