The stored modified date is correct.
Your problem is that the column is sorted by what you see, which does not include the time portion of the modified date. To have the time taken into consideration, you must change the template.
Unfortunately, the current version of calibre does not provide a way to display dates with times in custom columns. I interpreted this post as an enhancement request and have added a new format code to do that; the change should be in the next release. After the change is released, either remove the formatting template on your custom column or change the value given to format_date to 'iso', without the quotes. Examples:
or
Code:
{last_modified:format_date(iso)}