Are you sure you have transferred files successfully? The command line tool does not check data and gives no indication wether a valid nl file was received. Once it has received at least one byte, it waits until no more data have been coming in for a second and then saves that.
With the command line tool, the only way to validate a file is to send it back to a different bank on nanoloop.

To check the adaptor's and the software's functionality, please select the MIDI mode tab and set it to either SYNC or MIDI. It should immediately confirm with "SYNC (or MIDI) mode OK". If it remains "..." instead, something is wrong with the adaptor and/or the MIDI system. If that's the case, please try unplugging the adaptor, re-starting chrome and re-starting the computer.

If setting the MIDI mode works, the adaptor/webapp communication is OK. If the update still doesn't work, there is probably something wrong with the cable connection. It may be plugged in the wrong way (see image in the webapp for correct orientation), be the wrong type (only "8bit" / gb pocket/color compatible cables work, GBA cable does not) or be broken.

Everything is set correctly, and the cable I have is color.

I was able to move saves so the orientation is correct.

If setting the MIDI mode works, the adaptor/webapp communication is OK. If the update still doesn't work, there is probably something wrong with the cable connection. It may be plugged in the wrong way (see image in the webapp for correct orientation), be the wrong type (only "8bit" / gb pocket/color compatible cables work, GBA cable does not) or be broken.

in which way is the web app buggy and unresponsive? what happens?

if you don't run other MIDI software (including the command line tool and other instances of the web app in other windows/tabs) at the same time, it should be fast and responsive.

Whenever I try to backup or update, it seems like it can't read the cart or something. It says "waiting for data" or "press start+select" and nothing happens when I do.

if you don't run other MIDI software (including the command line tool and other instances of the web app in other windows/tabs) at the same time, it should be fast and responsive.

So I'm trying to update my rom but I'm running into a snag.

When I get to the holding of start and select, the nintendo logo never blinks after disappearing.

I've tried this on OSX (El Capitan), PC, and the web app (which is really buggy and unresponsive for me).

OSX shouldn't have an issue because I just sent and received save data with no problems.

What's wrong here?