I have started sync from scratch, cleared the smartphone contents and performed a full sync, in MSC mode. Since then, autosync worked properly.
Then, I have attempted to perform an autosync, with the phone connected in MTP mode (and exactly the same settings used for sync in MSC mode) to see if it worked properly; first of all, It took almost 4 minutes to allow MM to complete the "Scanning" phase (really too long), however as MM attempted to remove previous content in the smartphone, I had to forcibly terminate this as soon as possible (unplugged the phone).
Once I have disconnected the phone, exited MM, launched again MM and connected the phone again back in MSC mode, I have attempted an autosync and MM started syncing again some hundred tracks (probably deleted from the removal performed by MM in MTP mode). Unexpectedly some tracks took minutes to sync (I started believing MM hanged). Once finished I have disconnected/exited/relaunched MM and the phone and performed an autosync and since then MM will keep synchronizing 3 tracks (always the same)

I believe something has been scrambled somewhere, however I'm temporizing now, just to avoid the umpteenth full sync.
Finally, to makes things easier and more safe &reliable, I think that MM should:
- keep ONE unified list of sync contents: PC list and device list
- once the device scan is started (in MTP or MSC mode), look for changes on the device and update the device list accordingly.
- perform the sync based on the above results
This simple approach should allow for safe, fast & reliable syncs regardless the connection (MTP or MSC) AND should allow for proper syncs across multiple computers.
At least, at the moment there should be an option to rebuild device contents WITHOUT requiring a full sync to reset thing to work properly.
What do you think?