Popup is collecting emails but not subscribing in shopify?

 Welcome to the community @wellykicksnz 

3k subscribers in a month - congrats!

To your issue: 

Have you enabled your Shopify sync settings? The Shopify sync is necessary to keep your opt-ins and unsubscribes aligned on Shopify/Klaviyo. 

More info here on Shopify to Klaviyo sync and here on Klaviyo to Shopify sync

In Shopify when a contact opts-in to marketing, usually during the purchase process or a Shopify web form, the Shopify property 'Accepts Marketing' is set to 'true'. 

When a contact opt-ins via a Klaviyo form and is added to your target list, the Klaviyo property 'Email' is set to 'Subscribed' for that contact. 

Without the sync, there will be instances where a contact is 'opt-in' on Shopify and 'never subscribed' on Klaviyo, and vice versa. This sounds like it’s your issue.

Note that when the Shopify >> Klaviyo sync is enabled, it only syncs Shopify opt-ins to your chosen Klaviyo list "moving forward". Any Shopify opt-ins before the sync is enabled will still be 'never subscribed' in Klaviyo, unless they have also subscribed via Klaviyo.

To ensure you are considering ALL opt-ins when sending a Klaviyo campaign, create a 'Contact (opt-in)' segment that includes 'Accepts Marketing' = 'true' OR is in [your Klaviyo opt-in list(s)]

I believe the Klaviyo to Shopify sync backfills data to Shopify, however, I only ever send campaigns via Klaviyo, not Shopify, so please check that.

Hope that helps!

Andy