Did you ask to take it as lieu time and work extra hours on another day? Ask them to clarify on Monday. But honestly it sounds like they're using Bradford Factor which is based on occasions of absence, not hours of absence.
If you've only been there a few weeks I'd honestly say you've put your job in jeopardy, sorry. But most SME to large employers will automatically fail probation for anyone who has taken over a certain amount of sick days during probation (not including and condition or disability which has been declared.)
Migraine is a fucking bitch and mine got infinitely worse with stress. When I was splitting up with my then H I got at least 3 a week, at one point I collapsed in Sainsburys and knocked over a whole row of Pepsi 2 litre bottles :( My GP put me on amitriptyline and it was an absolute life saver. You must take it every day though.