Honestly, it sounds to me like it's behaving as expected. Shops and Rests are considered their own rooms in the code, not as being at the end of another room, so as you've described, you have 33 rooms in total with:
22/33 Normal (66% vs 70% target)
1/33 Challenge (3% vs 6% target)
1/33 Boss (3% vs 4% target)
3/33 Shops (9% vs 10% target)
6/33 Rests (18% vs 10% target)

As you remarked, quantities are quite good, distribution may seem to form a pattern, but that's kinda just how random works with low levels of options for variety. Now, if you actually see challenge rooms or boss rooms showing up at precisely regular intervals, that's another story, but in my experience they've been pretty decent, and from testing on my end it seems to be working well.
All that being said, I'm also working on completely redoing how I do level-type selection within the code, to try and clean it up, so it will be changing here anyway within the next few days