How are you updating inventory for the product / variant? Are you:
1. editing the product via the edit product screen in Shopify?
2. or are you using the incoming inventory / receive inventory screen?
I ask because Shopify currently only notifies our servers of inventory changes from situation #1 above - not #2.
For situation #1, it may take a few minutes for our server to update inventory on our end.
For situation #2, this isn't a limitation in our app but in Shopify.
The only workaround we have is to use the 'manually sync inventory' link in our app after receiving new inventory