Don't worry about it- You're right :). Just take it in the AM instead.
I've been trying to remember where I read it for you, but unfortunately I don't, after so many years of parsing through alternative research. If I do remember later, I'll find this post and append the information for you.
All I do remember is, it was from a source whose info I do know is trustworthy. They said 'do not take the oils later in the day, take them earlier on in the day, because they can actually cause trouble with your trouble if you take them too late in the day.'
I suspect that's exactly what you're seeing.
Like you, I had also noticed that the Cod Liver oil I take (2000 mg/day which I was taking in the afternoon or at bedtime) seemed to be exacerbating the stuff I deal with, and it was confusing me because I know darn well that Cod Liver oil is part of the solution for me. So I was, like you, quite concerned until I located that little piece of information while attempting to assist a friend with their own situation.