I have been experiencing the same problem lately.
It just happened again last night.
There are a few hundred that have registered successfully but it happens periodically where they will fill out the registration form and it will route them to paypal and pay - but no record was ever created.
This is the first event using the partial payment option - not sure if anything is related to that.
I have been using DT Register for a few years and never experienced this before - Just finished another event with about 200 people registering it was a pay now event and no issues.
so I am wondering if the two are related.
I have also been experiencing multiple times where people will pay on the partial payment after the 1st payment and it takes it in paypal but never updates the balance in DT Register.
Any help or any idea would be helpful.
Obviously the configuration of the server is correct or no-one could register and the directories are writable. many people can partially pay and it tracks it but it is random and takes a lot of work updating each day or week.