I use TMPGEnc frequently and never experienced the problem below.

As source, I use a 25 fps .avi file. However the frame rate in the
"Source range" window of TMPGEnc shows 30 fps if the "DirectShow File
Multimedia Reader" priority is set to 1 in the "Enviromental settings"
(VFAPI plug-in).

When this filter's priority is set to 0 or -1 (default), the "Source range" shows 25 fps.

Can someone confirm this?

TIA