In Reshade version 6.5.1—and even in some earlier versions—we're experiencing difficulty clicking on the Pip-Boy map to fast travel in Fallout 4. It often requires multiple attempts before the click registers successfully.This issue has already been reported by several users, such as:
I have this issue too. To click on a map point of interest I have to enter the Reshade menu with the Home key, select a point on the map, and then close the menu. This didn't happen with 6.2 so it started some point after that.
I can also not reach the top or the bottom of the screen during dialogs eventually. It doesn't happen immediately for me for at some point during the game. Forcing a reload of Reshade from the menu fixes this temporarily.
Fallout 4 uses swf files for their interfaces. Changing the Input Processing setting to "Pass all input to game when overlay is visible" did not matter.
Apparently this is related to input changes made after 6.2.0. Reshade had previously adjusted the game's handling of input which avoided these issues and this stopped being the case starting with 6.3. Short of a new option to adjust the game's handling of mouse input to whatever it was doing on 6.2 I don't expect there will be a fix for the problem, at least from the Reshade side.
So, It seems Reshade is coded to be handling input correctly while perhaps it's Fallout 4 which isn't, perhaps related specifically to those SWF interface files.
It's possible someone would need to write an F4SE plugin to avoid the issue but, short of that, I don't see a fix happening for Fallout 4.