Hi Aaron,
Do you have multiple BuyNow module added to your site?
Currently there are 4 places to enable/disable the "Hide Quantity" feature which are the following, please check to be sure they are not enabled:
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In the Cart Settings under General Cart Setup. Enable this if you would like to hide the “Quantity” textbox on the product listing page. This is useful if your business only sells to resellers that require prior approval before buying your products.
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At the product level in the Product Setup screen. When enabled, this feature hides quantity for a specific product. This is useful when setting up a product catalog only or do not want the user to change the quantity for a product. When hide price or hide quantity is checked here the price will be removed on following screens and confirmation emails:
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Product listing page
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Product details page
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Cart page
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Confirmation page before payment
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Confirmation page after payment
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User and admin confirmation email
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In the Product Details module Settings. When this is enabled “Quantity” textbox on the Product Detail page.
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In the Featured Product module. When enabled the “Quantity” textbox on the Featured Product module will be hidden.
Thanks,