In addition to what the JoS Guardian Power of Justice said, also try to notice how you are on a mental level when you start meditating on your chakras, because if you are tense or in any way in an anxious state, this can cause problems when you do power meditations or try to empower yourself.
It happens to me sometimes when I start meditating on the chakras and I'm in a tense state for some reason, or I already have the beginning of a headache, that it accentuates the headache more.
But this happens only when I do empowerment meditations.