When you save your package from BIDS, the values you have for all properties are saved in the DSTX.

If you have package properties stored in your SSIS Config table, those package properties are overwritten at runtime by the values stored in the table... The DSTX stored in MSDB, or wherever, never changes. So when you pull your package down from your server, you are seeing what was deployed, which was the DSTX you saved from BIDS.

Part of the Runtime, pre-execution phase of your SSIS pacakge is to step thru your various package configurations substituting the property value in the package with that stored in your SSIS Config table, for example.

Are you finding that when your package runs, your select properties aren't being updated to your table stored values?