Anyone else have hard time achieving rectal muscle fatigue/dealing with involuntary clenching?

Good question, I hope we get some guidance. In three years I have not been able to get that peristaltic movement!

One thing though that I notice is that my rectal contracting muscles do not fatigue easily in to a flutter/involuntaries as many talk about during stimulating contractions.I don't think that is unusual, for the most part you don't usually consciously contract those muscles except as part of the natural peristaltic contractions which take place in the midst of a bowel movement. The muscles with which you are more likely to induce involuntary contractions are the anal sphincter and PC/BC muscles, as those are under more conscious control.What usually happens is that at some point, the rectal muscles will begin to clench and tug on to the device. That clench holds and it becomes more comfortable to relax and let it hold there than it is to relax everything completely (like my body wants to pull it in and hold it).This is perfectly normal, if you look at the Milestones list in the Aneros WIKI you will see the following four lines ->
"...Involuntary clamping, without sense of climax
Involuntary clamping with hint of climax
Involuntary clamping with definite feeling of light orgasm (Mini-O)...
...Intensely pleasurable involuntary clamping that is clearly a Dry-O"
So what you are experiencing is well within the experiential path.
I've tried waiting over 30 minutes for the muscles to become fatigued but they just keep on holding. Should I regard the clench as a new baseline relaxed state and then re-start contractions from there?I wouldn't be concerned with expecting them to become fatigued, that clamping is an involuntary contraction in and of itself and is a milestone in your progress so YES it is a new baseline for your rewiring. Whether you re-start doing contractions or just enjoy the pleasure waves which are generated by the hold is your choice but I'd recommend you just focus on that hold and see if the pleasure builds from that position before you consciously try to force things along.
To others reading this, please remember what is said at the beginning of the Milestones list. ->
"Milestones are progress indicators in ones journey with the Aneros. It is important to note that each journey is a unique and personal experience. All of these milestones may not apply to everyone. Some men may whip right through them without realizing what they are, while others will skip many of them altogether. Every man’s pace with this is different; some will accelerate and then plateau, while others will move slowly through them savoring each achievement. Regardless, the journey is well worth it. Again, everyone’s experience is unique, so the order presented here is an approximation. Where you land is the luck of the draw."
You're doing well, keep up with the explorations!
Good Vibes to You !

Just relax and relax more... yes that is not easy. And no use chasing involuntaries.