The "Launch at login" flag is not saved in the Mega from the flatpak version.
I put it on, close the settings window, open it again and there is no flag. I use Arch x86_64 and Gnome 43.2.


$ flatpak info nz.mega.MEGAsync
MEGAsync - Easy automated syncing between your computers and your MEGA Cloud
Drive.
ID: nz.mega.MEGAsync
Ref: app/nz.mega.MEGAsync/x86_64/stable
Arch: x86_64
Branch: stable
Version: 4.7.3.0
License: LicenseRef-proprietary
Origin: flathub
Collection: org.flathub.Stable
Installation: system
Installed: 43,2 MB
Runtime: org.kde.Platform/x86_64/5.15-21.08
Sdk: org.kde.Sdk/x86_64/5.15-21.08
Commit: 80bd5f60ceea11d7cff62fca7fe5c9b84b133a3c7ac6e09408f0a38ab8658402
Parent: ad7bf83c064b88ecfb90260d7dfc20a15a6740dea30320f52c976aaadc232633
Subject: Update c-ares-1.18.1.tar.gz to 1.19.0 (d6b6b825)
Same problem here on Mint 21.2, Cinnamon 5.8.4, MEGAsync flatpak 4.9.5 -- keeps unchecking "launch at login", will not stay checked. It is listed/enabled in the OS's startup applications list, but it doesn't run at startup.
The package.deb download for Mint 21 from the MEGA website crashed constantly after installing, so not at all usable.
(Update: I uninstalled and installed the version in Synaptic, that one is working so far)
Are you able to add sync folder from the Flatpak version? For me it freezes and I can't add anything. I've tried on TuxedoOS and on my Steam Deck with no luck (from the flatpak version). Installing the Ubuntu version on Tuxedo works just fine
Same issue here with the the launch at login flag
Same issue on pop os
As a workaround the following works for me, in Startup Applications, add the following command: flatpak run nz.mega.MEGAsync &.