If autoscale cannot find the data it's configured to look at, it will set your capacity equal to the "default" configured in the autoscale rule.
As for what could explain the behavior you're seeing, here are a couple hypotheses:
1) There are two types of metrics in Azure today: host and guest; host metrics live in Azure-internal data stores and as such don't require a storage account to store data in. Guest metrics, however, do live in a storage account. So depending on how you added autoscale, you might have added host metrics instead of guest metrics? For more info, see this doc: https://learn.microsoft.com/en-us/azure/monitoring-and-diagnostics/insights-autoscale-common-metrics
2) As you can see in this template using guest metrics, for guest metrics the scale set must have the WAD extension configured to point to the storage account; it's probably worth checking that the storage account specified in the WAD extension config is the same storage account you looked for the table in.