Anonymous checkout problem: not all new accounts created

I'm having problems with the creation of new accounts during anonymous checkout. For some reason, almost 50% of new accounts fail to get created. I'm using it with a custom built module that integrates with GoCardless.com.

Everything seems to work with the order, which is created, and it redirects back to the site ok after the new direct debit is set up at GoCardless. Also both the admin, and the customer emails get sent out. The customer email includes a user name and password. However for those that fail they cannot login, obviously, because their account does not exist.

I'm having problems with this because I cannot find anything in the logs, and also I haven't been able to reproduce it myself yet. I cannot see any patterns amongst the orders that have failed and those where the account was created successfully.

Has anybody got any ideas?

If I cannot get to the bottom of this, I'm planning on using conditional actions, to run a test upon completion of checkout, to see if the account has been created, and if it hasn't, use some custom php to created the account.