If you could post a SysCheck it would help. Ill make a few suggestions.
1. Update to Wiiflow-Lite 5.2.0 if you haven't already "I'm using WFL 5.3.0 beta 6."
2. In Wiiflow Settings>Startup Settings
Force Load cIOS>On
Force cIOS Revision>Auto
USB Port>0
Mount SD Only>No
3. If the problem still exists, delete the wiiflow.ini or wiiflow_lite.ini located in
SD>apps>wiiflow>
If you have your apps folder on USB, check
USB>apps>wiiflow
If these do not solve your issue, post a SysCheck. There are many willing to help but you must provide information. Good Luck