Whenever you're doing column chemistry, it's important not to let the column dry, because air gets in, forms voids, and channels, and you lose resolution, and separation efficiency.
You've got to plug the bottom, or seal over the top, or do your workup first, so that a small amount of fluid is always remaining at the top of the column during all steps.
See if someone with a bit of experience can show you their method. Once you've done it wrong, you'll know how to do it right.