Anytime you take herbs that adjust your estrogen, you risk certain symptoms until you can figure out what is a good balance for your body type. Here is a site you should read over since you now know you are prone to migraines. It list the different phytoestrogen herbs that trigger them in some women. Both fennel and hops are on the list.
http://www.migraine101.com/phyto.htm
I think much research should be done on any herb you decide to take into your body. There are many things that might surprise you about an herb that is fine for one person to take and not for another. A good example is fenugreek. Most people don't know that it is in the peanut family, so if someone has peanut allergy then they should probably avoid it just to be safe.
Fenugreek is also a good example of how an herb can work two different ways for two different women. For some people it is great at treating migraines, but in others it can trigger them. It all comes down to your own personal body chemisties and hormone balances as to which herb is going ot do what for you.
The same goes with birth control pills also. There are so many different ones with different levels of hormones. One might work well for you, but another might cause massive migraines for you.
We are always always expeirmenting when we decide to take anything new into our body, whether it is something like herbs or something our doctor has suggested--either way it's a gamble most times.
I hope you can get it settled soon. As a migraine sufferer myself, I understand yor pain. Mine are my red alert that my estrogen is too high. thankfully as long as it's level, I'm headache free.
Good luck, Mel