I use it to auto-restart my computers and cgwatcher reboots via the registry without issue.
I don't manually execute any commands, and mining commences without issue.
I believe once you issue those from a cmd or bat re-issuing is just redundant.
Redundant after a re-boot ? I seriously doubt that ... If you shutdown/ restart your computer commands have to be re-entered... But I will try without I guess.
On a side note ... I am basically mining alone at
http://pool.cachecoin.net, someone come and join me ... 2 blocks found in the last 3 hours

Almost all the CACH to myself got very lucky ! But if one goes to 200% I will be mining for days !!! need more hash power !
I find the pool mining to be much more stable... When I mine P2P crashes are more frequent and I find the P2P nodes to be unreliable lately. Miner is contstantly waiting for new work.
Cheers,