Direct answer
System proxy affects apps that respect OS proxy settings, VPN mode captures more mobile traffic through the platform VPN API, and TUN captures network-layer traffic when the client and OS support it.
What to check first
Daily-use issues often sit between Clash and the operating system: proxy settings, VPN permissions, background restrictions, browser extensions and startup behavior can all override the profile.
- Check whether system proxy, VPN mode or TUN is actually enabled.
- Look for browser extensions, firewall tools or other VPN apps that override routing.
- Restart the client after changing DNS, TUN or startup settings.
- Read the tray status and logs before changing the subscription.
Recommended handling
Keep the troubleshooting path narrow: confirm the profile, confirm the selected node, test Rule mode, read the log, then change only the setting that matches the observed status message.
Practical notes
- Change one setting at a time so the result is attributable.
- Use logs and timestamps when asking for provider or community support.