You are breaking up the comment block before your endcode command.
## For: Something
#
# This proc initializes the GUI with meaningful values.
#
# \arg \c PROC HAS NO ARGUMENTS.
# \return PROC HAS NO RETURNVALUES
# \todo Harmonize var names
# \code
# proc ::IniGuiValues { } {
# THIS LINE IS BLANK
# set err [ catch { set LCIds [getSubcaseList] } res ]
# if { $err == 0 } {
# set ::GUI_LCs $LCIds
# }
# \endcode
proc ::IniGuiValues { } {
THIS LINE IS BLANK
set err [ catch { set LCIds [getSubcaseList] } res ]
if { $err == 0 } {
set ::GUI_LCs $LCIds
}