This functionality only is an issue with the Standard Edtion of Add2Exchange.  The Enterprise Edition works as designed.

 If the service is already started, (which it probably shouldn’t be if the Console is open) the program will not ask you to start the service

If the service is not running, and it does not prompt you, the machine must be a Windows Server 2008R2

And yes, that is a known issue.  This is the only real incompatibility with Win Server 2008R2 and this issue will be fixed very shortly with a maintenance release.

In the meantime, you can use two net start helper applications and you can set a desktop shortcut

They are installed where A2E is installed and explained here:

Make a shortcut to the desktop for these programs on the desktop of the Add2Exchange Service Account.  Unlike the Add2Exchange Console, these are just “glorified” net start and net stop utilities which can orderly start sql and can also stop the A2E Service and then the A2ESQLServer, orderly as before a MS update.

http://guides.diditbetter.com/a2e-guide/stopping_the_add2exchange_service_during_backup.htm?zoom_highlightsub=stopping

In the short run, before the fix, you just remember to start it when you Close the A2E Console,

Or you can use these programs as a temp fix for Windows 2008 R2.

Or you could even put a scheduled event to start add2exchange service.

If you subscribe to the RSS feed on the website, you will be notified automatically:  http://www.diditbetter.com/feeds.aspx

Please note to stay current. 

The most recent changes released (today) to Add2Exchange are big, for speed and reliability, and some fixes so go get current please using these instructions.  http://support.diditbetter.com/kb/a2e_219.aspx

For the current list of changes: http://support.diditbetter.com/kb/A2E_150.aspx. Be sure to find your version number and see what has been done after that.  If there have been mandatory changes since your release, then upgrade soon for reliability.

Hope this helps.