I was having the same issue (Roku 3, Harmony IR remote, stopped working when I installed a 32GB card) and think I found a work around though trial and error.
Install the SD card, skip formatting for now. IR remote likely stops working, that is ok.
Use phone app or point anywhere remote to do a factory reset on the box. Leave the card installed and all cables connected. Follow directions to set it back up and link to your account.
Choose to format SD card when setup is complete and it goes back to main screen. IR remote should be working at this point.
Once the format process is complete and channels are updated, the remote should still be working.
I have multiple Roku 3 boxes and one originally worked with the SD card installed. When I had troubles with the other I tried a bunch of combinations to get it working, and updating the software on both along the way. Then the box that originally was working stopped, so it could be related to a software update.
Doing the steps above put me on the latest software version (9.4.0 build 4200-04) and my Harmony remote is working with the card installed, so it doesn't appear to be a hardware issue. Must be some bug with the software.
Hope this works for everyone else experiencing the same problem.
The Micro SD card purchased from Roku (2GB) caused the remote to stop working and I am unable to format it. The card is inserted correctly with contacts facing up and pushed all the way in. I get the "Format card" prompt but the remote buttons don't work to select "format". The remote works fine without the SD card. I have a Roku 3 unit. I have read others having the same issue but see no solutions other than using a Roku app on a smartphone - I tried that and it doesn't recognize my device??? So that won't work. In the meantime the Roku 3 bootup at times is getting much longer and I thought the Micro SD card would solve this. I will buy a new smart TV before I spend more money on a newer Roku device.
I should add that the reset button inside the battery chamber doesn't help either.
How about a solution for this Roku?
Try formatting the card in your computer, if it has a card reader that can handle SD cards. After formatting, see if the Roku will detect and reformat the card successfully.
Windows instructions people have offered (don't know what would differ on other systems):
Do a slow (i.e. not "fast") format of the card via your computer. Select FAT32 and select it to use the default allocation size.
Re the Roku app -- it can't "see" your Roku until the Roku gets fully booted up and establishes its connection to your home network.
Thanks for your suggestion. I followed your instructions to a "t", slow formatted Fat32 the micro SD card in the SD micro adapter in my PC, re-installed the card in the Roku 3 and was again given the request to format or cancel. However no remote buttons would work so I could do neither. As far as using the Roku app on my iPhone, I did try it with the Roku 3 fully booted up and it was not recognized.
It's probably time to buy a new & "Smart TV" and just skip this Roku nonsense.
I've encountered this issue with my Roku 3 (4230X - Software version 9.4 - build 4200-04).
For the sake of clarity here is what I'm seeing: When the 32GB microSD card is installed in my Roku 3 the IR remote does not work. When the card is not installed the IR remote works great.
Here is what I've tried thus far:
Restart via software.
Restart via unplugging power cord.
Factory reset (Unfortunately I read the previous post after I'd already formatted the microSD card so I did the factory reset but without the formatting step)
So far none of these things has worked... any suggestions are welcome.
Same thing is happening with my Roku 3. For me it only happens when the microSD card is installed. I'm able to navigate with the app on my phone.
Here's another thread about it.
https://community.roku.com/t5/Remotes-Accessories/Added-SD-Card-Remote-no-longer-works/td-p/593683
If you can wipe the card and try the steps I posted above in the thread, it should get things working for you. I have no idea why it works, but I did it on multiple systems and my Harmony remotes work great on all of them now. Hope it works for you as well.
SOLVED Finally!
Ok, here's how I solved this with the micro SD card installed & formatted and the remote working fine with the SD card installed.
1) With everything OFF, install micro SD card contacts up. Then turn on TV & Roku devices.
2) Screen will show prompt to Format the SD card but remote will not work. Remove battery cover on remote, point towards Roku unit and press and hold the "pairing button" until the light next to the button flashes (if the remote has a light), otherwise hold pairing button for about 5 seconds. Then the remote will take about 20-30 seconds to finish "pairing" back up with your Roku unit. The screen will tell you when the "pairing" is complete.
3) The remote will now work but the SD card is still not Formatted yet. Turn off/unplug the Roku from power and wait 10 seconds and turn back on. The prompt to Format the micro SD card should appear and the remote will work to select "Format". If the remote doesn't work yet, re-pair the remote and start the Roku reboot process again.
You can verify that the micro SD card is installed and formatted by clicking on Settings>System>About>click to the right until you see your Roku account and at the bottom it will say Micro SD card and a % used and total memory used of the card total. Mine says 7% used (o.1/1.9 GB) for a 2 GB micro SD card.
Now, why in the heck can't Roku give us instructions like that??? Oh, silly me, that would make sense - that's why!
First, Thank you very much for all the help.
I wiped the card and went through your steps exactly as posted and my IR only Roku remote still is not working.
Even with the work around this is clearly a bug that I'm hoping will be fixed in the next release of the software.
Any further feedback or workaround ideas would be welcome.
Thanks!!
It became clear to me that when we add a micro SD card to the Roku unit it changes the hardware enough that the remote is no longer paired to it. And so we then have to re-pair the remote to the Roku unit. I have the Enhanced Remote which is identified by it having the "Pairing button" and a light that flashes when the pairing begins after holding the pairing button down.
Since you have the IR remote I would recommend trying the troubleshooting steps specific for the IR remote listed on this page below. In addition to what they suggest, I recommend turning off/unplug from power the Roku unit and remove the batteries from the remote. Then after 10 seconds plug the Roku unit back in and wait for it to boot up. Then reload the batteries in the remote and see if it pairs up now. Good luck!