Since doing the upgrade I haven't been receiving order e-mails, nor have customers been receiving their order confirmation e-mails. Contact us form and order history e-mails are received with no problems. I didn't change any e-mail settings under System>Settings>Mail after I upgraded - new order alert e-mail has always been on and this hasn't changed.
I have Qphoria's Paypal Hosted extension and Get Clear Thinking's product based shipping extension installed. I contacted Qphoria yesterday as I thought it was an issue with this extension, but I've not received a reply as yet. I enabled the debug on the Paypal Hosted extension, but there doesn't seem to be any errors on there.
I've read through lots of posts and tried almost all the 'fixes' I found with none of them working (e.g. system>library>mail.php, adjusting line 97). I have now tried changing all the e-mails settings, again, with no luck at all getting admin e-mails to send. I also re-upgraded everything again this morning to see if the upload of files yesterday was the problem, but it didn't make any difference.
I'm currently having to manually send all customers an order confirmation e-mail and manually send myself order confirmations, which is tripling the work I have to do when processing orders.

Can anyone help me with what the problem might be?
Summary of what I'm using:
Opencart: 1.5.6.4
Journal 2 theme: 2.6.0
VQMOD: 2.5.1 - standard
Paypal Hosted latest version
Product based shipping (getclearthinking)