Native OneDrive not following configuration that is displayed with --display-config, causes constant pop-ups

I installed native onedrive (not from PPA). Auth, started a sync.

Using /home/user/ as the sync_dir so it uses the Documents Pictures and Desktop directories for my user.

I set it to skip dot files, and also to check for .nosync, then I touch .nosync files in the directories I did not want synced like Downloads, VirtualBox\ VMs etc.

I keep getting these notifications for OneDrive no such file or directory, but they are all from dotted directories like .config or .cache, which I thought were ignored because of the skip_dotfiles being true.

Since this started happening, I touch .nosync files inside of .config and .cache, and have also started using the skip_dir parameter adding .cache|.config and have restarted daemon in between each but I still get the messages.

I did set it up as a service with

sudo systemctl enable onedrive@user

sudo systemctl start onedrive@user

Here is output of onedrive --display-config (run as 'user')

Configuration file successfully loaded
onedrive version                       = v2.4.13-1build1
Config path                            = /home/user/.config/onedrive
Config file found in config path       = true
Config option 'check_nosync'           = true
Config option 'sync_dir'               = /home/user/
Config option 'skip_dir'               = .cache|.config
Config option 'skip_file'              = ~*|.~*|*.tmp|sdc*.txt*|securelink*.log|desktop.ini
Config option 'skip_dotfiles'          = true
Config option 'skip_symlinks'          = true
Config option 'monitor_interval'       = 300
Config option 'min_notify_changes'     = 5
Config option 'log_dir'                = /var/log/onedrive/
Config option 'classify_as_big_delete' = 1000
Config option 'upload_only'            = false
Config option 'no_remote_delete'       = false
Config option 'remove_source_files'    = false
Config option 'sync_root_files'        = false
Selective sync 'sync_list' configured  = false
Business Shared Folders configured     = false

Here is example of what is constantly popping up on my screen: screenshot of error messages

System is a fresh Kubuntu 22.04

Linux katana 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

Thank you for the response. I have changed the config to use /home/user/OneDrive as sync root, created the soft links from /home/user/Documents (target) to /home/user/OneDrive/Documents (linkname) for Desktop, Pictures, etc. When I do a dry run it all seems to go fine, it shows Documents/ ... and not OneDrive/Documents for the linked folders. However when I run onedrive --synchronize --resync it fails:

$ onedrive --resync --synchronize
Configuration file successfully loaded
Configuring Global Azure AD Endpoints

A database statement execution error occurred: disk I/O error

Please retry your command with --resync to fix any local database corruption issues.

Segmentation fault (core dumped)