Di2 Button Setup Prompt

My apologies for the late response.

The junction box is located in the right hand side bar-end. I'm not exactly sure how they are wired up together. Never really paid attention to it.

The D-fly is exposed at the center of the bike the in front of the stem. I'll see if I can snag you a few these photos.

I haven't had a chance to write it since the last time so I will keep the final verdict off for a while, but hopefully it is just a faulty D-fly.

I have a bar end junction boxed originally a Y cable (EW-JC130) connected the two shifters leaving a port free on each shifter. A d-fly module (exposed) was connected inline to the cable to the junction box B which is located above the bottom bracket. This connects the battery to the front/rear mech and the shifters.

I had an issue with junction box B after about a year and the part which caused a similar issue to you was Y cable because its as under bar tape and eventually was damaged.

Hey Rob, just an update. It's been stable for the most part. I had two random prompts over the past few weeks, which is pretty decent all things considered.

After the latest 1040 update things went loco for a bit. I wiped out the Garmin unit and it seems to be behaving better.

With that being said, as to your question, I do not have a Y cable. However, I do believe that some of the cables may be damaged. When I got those prompts, it was when my handlebar either swung to the side while I was carrying the bike or when I hit a very rough bumpy section.

I also realized recently that I've been having significant battery level drops which makes no sense whatsoever. Either the battery is going bad or there is something in the system that is draining the battery.

I topped it off this past Friday to 100% did not ride on Saturday and went for a ride today. After about 20 miles or so I stopped and happened to look at the stats and the battery level was down to 80%. That is most definitely not normal.

Since I don't have the time or patience to run back-and-forth to the shop and troubleshoot I've asked them to provide me with a quote to overhaul all the wires and swap out the battery. Any issues after that I can throw it at Shimano's and the shop's head. (We did a battery test the previous time I was at the shop and it showed no issues, but I don't know how much stock to give into that.)

The only thing I didn't do was check battery levels with the Shimano app, I never use it. I go off with the Garmin gives me. Hopefully it's not the Garmin that's giving me bad readings. However I did have one episode recently where my DI2 completely dropped dead (The only warning I had about the DIT battery running Glo was probably an hour or two before it completely crapped out) and had some warnings on a different ride recently before the firmware update so I'm assuming that those readings are fairly accurate.

FWIW I have same issue on Ultegra 12 speed Di2. Randomly prompting for setup (sometimes frequently, sometimes not at all) - happened on my 1030, and still happens on a new 1040. It also occassionally gives me a Di2 battery critical warning (when battery actually fine). The Di2 itself would generally work fine, but - as you say - feels like there are occassional laggy rear changes.

Have seen suggestions elsewhere that it was caused by a bad battery, but tricky to diagnose. Pain for me is the battery is in the downtube so would need to remove BB to access it and check connections (or replace). 

I've also noticed a software behaviour difference between the 1030 and 1040. On the 1030 if you clicked the buttons on both levers it would work out they were already setup and remove the message. On the 1040 the setup message doesn't go away.

Hi, get your local bike shop to run the SM-PCE02 tool through the Di2 junction box, this will give them a view of what the issue is. 

Yeah... not fun.

Will test things again next time I'm around and do complete cable swap to see how things behave.

If the issues continue, then battery swap as well.

Considering the bike was purchased in 2016 and has over 63,000 miles on it I'd say that the DI2 is a fairly robust system for the most part. (I also ride the bike in all conditions. I am not kind and gentle with it. )

The battery was upgraded in 2018 in order to be compatible with the D-fly that I added on along while swapping from my mechanical shifters to hydraulic. 

I believe that all cables are still original from the install date. Same goes for junction box. (Bar end)

I did manage to kill one FD and one RD in the past year or two. (Meaning each one lasted for about 50,000 miles or so before failing.)

Hello all, I just wanted to provide a final update.

After noticing (on a few occasions and charges) that my DI2 battery was draining far faster than normal I decided to rip almost everything out and have it replaced.

My mechanic swapped out all the cables and we also changed the battery.

Since June 14, I have logged 700 miles on the bike and from the initial charge the battery percentage is currently sitting at 70% and I've had zero button setup prompts. *knock on wood*.

I didn't have the time nor the patience to start doing things piecemeal and figured I'll just take the financial hit and hope for the best. So far, that seems to have been the right call.

That is all. Cheers!