CB Listed Modified Date Does Not Match Directory A couple questions:
1. Why are you using Custom Mode? Is there some use case you are looking to solve? If not, you should use Advanced Mode as that mode gives you the greatest control over backup data, versions, retention, etc.
2. Why are you using Glacier? Glacier is for long-term, archival data - data that you do not plan to access, but need to have it saved just in case. Restoring data in Glacier can be expensive and can take hours to get the data ready for a restore. Also, if you back up to Glacier directly, then it's much more difficult to get a file listing in a timely fashion. You also have a 90 day retention requirement in Glacier - meaning, if you delete your data before 90 days, you are charged the remaining days by Amazon. But, if you want to simply back up this data once and keep it for years or you have data that you simply need to keep long term, then Glacier is a good solution - although I would still recommend you back up to S3 - Standard and move the data to Glacier using a lifecycle policy.
So, to help you, I need to better understand what your needs are with this data today and going forward. And then I can recommend the best solution for your needs.