In FileAssociation.nsh there are two lines that I believe should be changed (the first and last of the following three):
WriteRegStr HKCR "$R0\shell\open\command" "" '"$R2" "%1"'
WriteRegStr HKCR "$R0\shell\edit" "" "Edit $R0"
WriteRegStr HKCR "$R0\shell\edit\command" "" '"$R2" "%1"'
This should be:
WriteRegStr HKCR "$R0\shell\open\command" "" '"$R2" %1'
WriteRegStr HKCR "$R0\shell\edit" "" "Edit $R0"
WriteRegStr HKCR "$R0\shell\edit\command" "" '"$R2" %1'
Parentheses should not be around the %1. When they are there, the parameter is not set, and the file will not open in the desired software.