Are you running Automatic Reprice or are you repricing using Get New Price Data and Reprice?
If you are only using Get New Price Data and Reprice make sure not to skip the step of uploading the price changes to Amazon. To do this click 'Upload' > 'Update prices for existing listings':
When you upload make sure you specify which items are to be updated; if you select 'All items marked for export' make sure that the items are checked in the 'Export to Amazon' column.
If you are using Automatic Reprice or if you are are already uploading the price changes as described above but the prices still remain unchanged on Amazon then there might be errors when Amazon is processing these uploads.
To verify this please select a sample of items for which the price doesn't change on Amazon, reprice them using 'Get New Price Data and Reprice', then click 'Upload' > 'Update prices for existing listings', make sure to upload only for the selected items:
Save the Batch ID of the upload you just made. It will show up in the bottom-right corner of the SE Plus window:
Now go to your Seller Central account, click Inventory > Add products via upload, and in the second half of this page check the processing report with the same batch number. If the processing contains any errors open it and see what the error messages are saying. If they are unclear send us the processing reports and we'll further investigate.