Recognizing that I am replying to myself... but... figured I'd share the final result here.
So, after the transmission cooler was replaced by Mini Downtown (which, btw, I STRONGLY RECOMMEND AGAINST using Mini Downtown in Toronto. They are extremely rude, the manager there Justin is not helpful, he is abrasive, angry, and doesn't like helping customers; they forgot to clean the underbody of the car, and it leaked residue all over my condo garage. Returned, was cleaned up, and I started driving it again), the problem persisted. The cooler replacement did NOT fix the vehicle despite Mini Downtown's insistence that it would.
Recently, I finally had enough and took it to a different dealership. For $110, they did a full diagnostic, checked fluid levels, end to end check of the car, and they decided to perform an adaptive reset (done by them hooking up to the ECU and issuing an adaptive reset) on the transmission. The car now drives beautifully! If you are in the Toronto area, I strongly suggest Mini Vaughan for your service. They treat you with respect and they don't try and charge you for unreasonable things. Mini downtown argued they had to always charge me to check the fluid level in the transmission, even though Mini Vaughan did those types of things for free, and even though Mini Downtown had just done a repair of that very same component. Stand behind your work, Mini Downtown, or you lose customers. This customer is definitely never going back there. Vaughan won by business.
One comment for those who may think I'm being unreasonable. I called Mini Canada and spoke to them about what happened. They advised me to try Mini Vaughan as they get complaints every day about Mini Downtown. So, at least know I'm not alone!
If you have a 1st generation R50 with transmission issues, I strongly suggest you always check the following things:
- Check your fluid level. This is the #1 thing I'm told that can make a transmission act strange. When they refill it, make sure the fluid comes out clean - if it is, it's an indicator of a healthy CVT
- Battery Voltage; if your battery is very old, replace it. Transmission needs a good strong charge to engage properly
- Latest flash of your ECU. Make sure you are up to code.
- Check your cooler. If the pressure is low, it could explain your issue. I definitely had a leak, but it wasn't what caused it
- If you are not the first owner of your R50, and it's many years old, try a transmission adaptation reset (known as a "drive cycle"). It learns over time how you drive, and if you dramatically change your habits, and especially if you do transmission work (cooler replacement), a drive cycle seems obvious. Too bad it wasn't obvious to the dealership I paid so much money to!
Thought I'd give everyone an update on this in case someone else has the same issue.
What I tried:
1) replaced the battery. Car itself started acting better, but the issue persisted
2) Had a voltage test done from battery to ignition. All clean.
3) Had a computer diagnostic. No codes
4) Did an ECU flash to the latest Mini dealer provided ECU. Car drives better (smoother) but issue persisted
Finally, after an oil change, I saw some fluid on the ground that turned out to be transmission fluid. I had Mini check it on Friday, and it's the transmission cooler that's cracked, slow leaking fluid, and there are cracks in the lines to the cooler. This is causing both transmission fluid to leak, and for decreased pressure in the transmission. They suspect that this is what is causing my transmission to not engage on a cold start, the pressure takes time to build up. They also found about half of my fluid missing from the closed system, which they are flushing.
Moral of the story: If you find that your transmission is not starting on a cold start, start with the battery, then check your transmission cooling (fluid) system.
PS: This type of repair (cooler, adapters, coils, etc) costs $1300 or so, of which $850 is parts and ~$300 is labour.