So sorry to hear that! You can always feel free to ask as many questions as you have. 
 
Yes, it's true that everyone's different, but a 10 day flare doesn't sound normal. Have you emailed Dr. M about this? She says that although a new protocol may not make you feel better initially, at least it should not make you feel worse. And if it does make you feel worse in any way, there's probably some adjustments she needs to make. 
 
I learned this the hard way towards the beginning of my treatment by enduring major discomfort for about 4 weeks because I thought it was just my body assimilating the new herbs. Dr. M was alarmed I had waited that long to bring it up and told me to stop the new herb immediately. 
 
Since then, I have gone through ups downs, and we've had hit and misses with the herbs. When the herbs are wrong, they usually esacalate my discomfort over the course of a few weeks (making it difficult to catch them in time, until I am in an all-out flare). But when they're right, they immediately have positive effects on my body, usually within the same night, or within 2 days at most.
 
And as for your poll, I felt better almost immediatedly (def. positive change by week 1). And by week 3, I had stabilized so much that she upped me to List 2. BUT then I got comfortable around month 3 when I started List 3 (and got married) and started being very inconsistent with the diet. I drank and ate sweets at different wedding-related events. I'm now in month 7 and I'm FINALLY getting back to where I was back then (in month 3). So, please trust me, that even in the darkest hour, Matia WILL find the right combination for you -- just keep communicating with her and keep a well-detailed journal to give her the best information possible. 
 
Lastly, in this last round of protocol-changes, I asked Dr. M if I could take a break from the herbs for about a week, to rest from the dizzying pace of change (and subsequent flare-ups from using the wrong herbs over and over again). And she said "of course!" Funny, it never occured to me that I may actually have a choice in taking the herbs or not. I took my break (and felt better), then when I started the new protocol, I have started feeling even better. So, if there's ever a time you think the herbs are absolutely what's making you sick, stick your hand up and ask to stop! I'm sure Dr. M will say yes and let you get back whenever you're ready. (but of course, just consult with her first). 
 
Best of luck.