Confused....labral repair.

I'm 5 weeks out of a Labral tear repair, with Bone work for FAI (Pincer type). (I had it done by the fancy guy in Colorado...)
I'm apparently doing alright, I am walking though I still limp (I limped for 7-8 months before the repair so it's hard to un-learn).
I still have a lot of pain in the groin, starting at the adductor tendon area and then radiating up into the groin. My Surgeon said it was a little complicated because I did have the tear, but I also have a very tight Psoas, and some sort of adductor tendonosis.

I just had a follow up visit and he gave me the PT protocol. I am in PT 2-3 times a week with a DPT. He seems good but.... When looking at the protocol, I am not doing really anything on it. I am doing other things which are not on the protocol and then not doing other things. And It is not like we are just a week behind or something, it is just "different".

I'm not sure what to think. I want to do the exercises on the protocol as I think I have the best chance to succeed this way, as my PT has not done tons of these pts.

The obvious thing would be to ASK why, but, I can not figure out a way to do so without irritating him. I had 2 weeks with the Manager of the clinic and I found her to be following my protocol entirely and I liked her better, but because she is the mgr, I know I can't have her back. I am just not really trusting this person even though I've been with him since prior to the big trip out to the surgery and back....
   People are so sensitive, and I am extremely anxious abut my recovery. What would be a way for me to discuss this without upsetting the apple cart? (I live in a small town, and everyone knows everyone, so I really want to do this in a way that is gentle, and not accusatory, though I feel a little accusatory at the moment.) I know that sometimes people do things differently and DPT's can be independent practitioners, but, this seems off, or am I just being overly concerned? What do you think?

Thanks Ask a PT!
What eventually happened was that I saw the manager and unfortunately could not contain myself...I ended up crying my eyes out. She seemed surprised that we were not following the protocol, as it is a new procedure for this office to be doing.   She talked to him, and oddly, he actually watched me do all the exercises today and we seem to strangely be doing what is actually on the protocol. Now I can see I am about 1 week "behind" which is no biggie since it is a hugely long recovery. and 1 week out of 5-6 months is just not something to get too excited about!   
Feeling much better, well...after pool running feeling real sore, but still better!