The publication process consists of the following steps:
Builder generates final website files and tries to publish only those that were modified after previous publication.
After publication of changes builder tries to run a script on published site and check in this way whether all required website files exist on the hosting.
If (2) ends with "false" response (that is eventually not all files exist on hosting), builder re-publishes all website files.
Sometimes, builder gets stuck on step (2) (or takes much time - ~1-2 minutes) since connection to the end website can be problematic. In many cases, firewall on hosting server blocks builder IP on port 80. Due to the following, connection hangs until timeout is reached and builder tries different IP to connect. To avoid such problem make sure that builder IP is whitelisted on port 80 in hosting server firewall.