Not sure what additional information would help:
Ver. 4.2.3 (Build 494) - but the problem is the same on every version and has always been there. The server you connect to is irrelevant.
To recreate - select Commands|Synchronize... and set up synchronization of a remote site to the local directory. The settings are irrelevant.
As the program moves through the list of directories synchronizing, a connection may sometimes be lost for whatever reason. WinSCP asks if you want to reconnect (or does it automatically after a few seconds), but the synchronize... command doesn't pick up where you left off the way that transfers now pick up where they left off.
Instead, you have to re-rerun the synchronize command from the beginning. When trying to synchronize a large site, this is extremely problematic as it can take half an hour to compare all the directories, and having to re-run the whole thing from the beginning after 25 minutes can take all day.