Di2 Button Setup Prompt

Which groupset are you using?

My apologies for the late reply. I also did some additional troubleshooting and it seems that when I get those disconnects prompts, the LEDs on the EW-RS910 flash.

This leads me to believe that it may be some sort of issue with the DI2 and not the Edge 1040. What say you?

ok pretty much the same set up as me. My reply regarding an issue I had on another thread seems to be missing so I will share.

I had an Edge 1030 plus. One day it started with the set up di2 buttons has you have. Sometimes it would be happening every minute and other time not all. I checked all the cables and reconnected the battery but it didn't really make much difference. One day my usually reliable 1030plus crashed and I lost a big chunk of my ride. I don't think the two issues were related but cant be sure. I suspect that the Varia was to blame. Later I performed a full factory reset on my device and the stability returned but the di2 button prompts were still annoying. 

I was looking for an excuse to buy an Edge 1040 and after being offered a good deal I went ahead and purchase done. The di2 prompts seemed less but there were still there.

My shifting performance seemed ok.

A few weeks later I packed my bike for a short flight for an event in nearby Langkawi (Malaysia). During the post arrival build up in my hotel room I found that when I connected the battery the system was dead and wouldn't charge. After trying a few things it was clear that there was a loose connection or bad cable but I didn't know where. 

Luckily the only bakeshop on the island were able to look at it and found that the Y cable under the bar tape seemed to be the culprit. He didn't have a new part but seemed to get it working. Late in the day after testing near the shop it failed again. Luckily he had one longer cable so we wired that direct from d-fly to the right shifter and I used sync 2 mode for the event without any issues. Upon returning to Singapore I had the faulty part replaced. 

I didn't have any LED's light up like you so it maybe another 

Thank you for the information. This is good to know.

There was one other thing I noticed... when the error would pop up and I would try to shift the rear cassette I would have glitches. It's quite intermittent so it's a bit frustrating. I also noticed that it happened a lot going over rough sections or sharp turns (mainly to the right). That's why I'm thinking it's a cable issue. I mentioned the flashing lights to my mechanic and he had never encountered that before so he'll be reaching out to Shimano as well.

It's confounding and annoying. I never had this issue until recently. It's been rocksolid up until then.

Once again, thank you for your response.

Hi, try reaching out to the guy on https://bettershifting.com as he’s really helpful and full of Di2 knowledge. I have almost identical setup as yourself and no issues with the setup. I know it’s annoying but have you tried a reset already on the 1040? Latest firmware on 1040 etc?

Thanks for the information. I did not bother with the Edge1040 reset as on my last ride I noticed that when the prompt would come up my shifters would freeze up for a while as well. Clearly it had nothing to do with the Garmin edge unit and the fault seemed to be somewhere in the DI2 set up.

interesting note: when I held the bike in my hand and shifted gears, I would also get the flashing lights (solid green for a second or two then red and green together).

With that being said, I brought the bike into the shop and my mechanic did all the standard test via the software, everything passed with flying colors.

He ended doing a full disconnect and reconnect of all cables and that seems to have solved the issue.

He also noticed two areas where the cables came out real easy when he disconnected them.

Here's to hoping it stays well-behaved. :-)

Last year a friend of mine had basically the same intermittent issue just as Rob W describes. Also ended up being a bad di2 cable.

Update: The following day the issue came back. I reached out to my mechanic and we swapped the D-fly.

(This time I was also able to capture some video of the error message and then bring the camera to the junction box where you can see the lights go on. Solid Green then Red and Green together.)

Hopefully this resolves the issue. I'll keep this post updated after a few more rides.

Thanks for sharing. 
I would also check / change the junction boxes. The shop told me that the one near the bottom bracket can be troublesome.
Are you cables running fully inside the bars? Do you have the Y cable or are you using a different set up?