Ususally a string will 'creep' out of tune if there is something that prevents the tension from being distributed evenly along the entire length of the string.

The most common cause is the string being 'pinched' by the slot in the nut. This prevents all of the tension change being made by the tuning machine from appearing on the string. Some of the change is 'stored' between the nut and the tuner, and gradually gets transferred to the rest of the string. This makes the pitch creep up or down from the right setting. You can test this by plucking a string, and pressing on the string between the nut and the tuner. The note should go up, and then return to proper pitch when you release it. If it stays sharp, the string is being pinched by the nut slot.

You addressed this possibility by filing the slot, but use the 'press & release' test to verify that the slot is good, now.

The same problem can occur between the bridge saddles and that end of the strings. You can check this with the same press & release test.

Another possible cause, is the post of the tuning machine. If the suface is a bit rough, and the string is wrapped around too many times, the same tension storage thing can happen. If you don't 'lock' the string at the post, it may tend to slowly pull out, especially if there are not enough turns on the post.

If you find out what's making this trouble, please post here, so we can all learn from your experience.