Shortcodes are showing in browser and in emails sent to customer

On the site https://dev2.xbm-hosting1.com/cart/ most of the jigoshop pages: cart, checkout, etc. so the shortcode near the top before the content. Also the auto email shows all the shortcodes to the customer:

“Thank you, we are now processing your order.

[is_cheque]

We are waiting for your cheque before we can start processing this order.

[cheque_info]

Total value: $93.50

[else]
[is_bank_transfer]

We are waiting for your payment before we can start processing this order.

Bank details

[bank_info]

Total value: $93.50

[else]

[is_cash_on_delivery]”…

Is there a way to fix this problem?

Thanks,
Ann