Its possible to make synchronization happens in background (without the sync pop up window)?
There are already some users which asked this. Its a question of general strategy. In my opinion the user SHOULD KNOW that the phones gets currently synced. This is important to avoid problems
Its possible to make MyPhoneExplorer sync every 30 minutes (for example) (I'm speaking about syncing calendar and not everything)?
Its not possible with MyPhoneExplorer (cause its also against my strategy) but you could use the taskmanager to create a 30 minutes-poll. MyPhoneExplorer is also able to accept commandline parameters (take a look at the FAQ)