The OP's problem with the shared connection can probably be solved just by unchecking Setup > Connection > Connected while Idle. This will stop alt.binz hogging your server connections when it's done downloading.
The solution to the second problem is a bit more involved. I have a similar need to schedule a wake-up overnight, check if anything needs downloading, then shut down after downloading is finished. The key is to enable this option: Setup > Miscellaneous > Enable status in Xml file. Then for your scheduled task, instead of starting alt.binz, run a batch file that can monitor the altbinz_status.xml file in a loop. Here's a very crude version:
:start_altbinz
start "" "C:\Program files\Altbinz\altbinz.exe"
@ping 127.0.0.1 -n 30 -w 1000 > nul
:check_status
find "<ETA>Unknown</ETA>" "C:\Program files\Altbinz\altbinz_status.xml" >nul
if %ERRORLEVEL%==0 goto exit_altbinz
@ping 127.0.0.1 -n 60 -w 1000 > nul
goto check_status
:exit_altbinz
taskkill /t /im altbinz.exe
You can also manually disconnect alt.binz by changing "<connect>true</connect>" to "<connect>false</connect>". To do that with a batch file, you need to use a bit of vbscript or similar. Then you can use command-line utilities like poweroff.exe to shutdown immediately after.
Actually, all of this is much easier to do with Powershell, the MS replacement for CMD.exe and .bat files. That's what I use now, anyway, and I can share my scripts if that would help.
-Hecks