Hi,
The cause is definitely not the fact that a previous order was created. At least, in HikaShop's core code, there is nothing which would do that.
If the email doesn't appear in the email history, then it indeed means that it wasn't generated. In that case, the most likely cause is that the page processing crashed before the email could be sent but after the order was created OR that a plugin turned off the email notification flag.
Just after the order is created, and before the email is sent, the only thing there is is a call to the trigger onAfterOrderCreate so that plugins of the groups 'hikashop', 'hikashoppayment' and 'system' implementing that trigger can act upon the creation of the order.
So I would recommend reviewing these plugins. The fact that a previous order was created might help trigger a malfunction in one of these plugins for some reason. If you have custom plugins or third party plugins integrating with HikaShop, I would suspect them first since no one else reported a similar issue.
Also, the best thing would be to check whether or not you are able to reproduce the problem consistantly. If you are, then that's great. Unpublish the most likely plugins one by one and reproduce the problem). If you don't get the problem while one plugin is unpublished, then it must come from that plugin.