For me wired syncing was working fine in older days with msc protocol (phones and dedicated mp3 players).
With newer phones things got quirkier...
I ended up just removing the SD card from the phone and syncing directly to it.
Just got a new phone yesterday. Synced wired from MC and it worked 98%. Out about 200 albums, three albums behaved strangely.
-- They did get transferred on the first run however, on sync re-check they were marked for deletion and re-syncing.
-- Upon re-sync they got transferred but the previous copies were not deleted but renamed to xxx.mp3.dup#
-- Next re-sync would add another copy of xxx.mp3.dup#
Interestingly all those 3 albums were CD #2 of 2CD sets (I have other 2CD sets but they synced OK).
Anyways, mwillems, I tried FolderSync (thanks for the tip!). It worked but was very slow.
I tried MyPhoneExplorer (also via wifi) from the PC side and it was 10 times faster! (5MB/s vs 500KB/s).
max
The android application "foldersync" can do exactly what you want using, for example, a connection to an SMB share or other share on your computer. It will sync on a timer or subject to conditions (only on wifi, only when plugged in, etc.) or both. You just need some kind of sharing setup on the host PC (foldersync supports most open standards like smb/cifs, s/ftp, dav, but also supports several proprietary filesync services like dropbox). There's a free version (or there used to be), but the $2 I spent on the full version was probably the best money I ever spent on an android app.
I also had miserable issues with wired syncing before figuring out a wireless solution. Now I use JRiver to "sync" to a directory on my harddrive, and then foldersync just wirelessly and automatically pulls everything onto my phone the next time I charge my phone (so I don't have to worry about it hogging bandwidth when I'm using my phone). Once you set it up, it's magic.