Have had this issue a few times and not sure what's going on.
Using the Data Import Wizard fields just won't update. Most recently, wanted to update a custom field on Account. Uploaded a csv with Account ID and the field to update (numeric, custom field; pretty standard). Everything mapped. Uploaded with no error, yet the values for the field just did not change/update.
Have searched the forums, but still no clue what could be causing this as I can't find anyone else who's reporting this problem.
Used dataloader.io and it updated the field just fine, so no huge issue, just bugging me what could possibly be causing this.
Whenever you update your account make sure to click the box
update existing account informationand that should do the trick!