You have 4 or 5 scripts in the supply.txt file that are described as "Axis Disrupts Merchant Shipping..."; however, the way they are scripted they only apply to German units.
This should probably be updated to consider all Axis Raiders (per the description).
See the following:
{
#NAME= Canadian Shipping Near Halifax Disrupted By Axis Raiders (Continuous)
#POPUP= Axis Raiders Disrupt Production At The Springhill Mines And Halifax
#IMAGE=
#SOUND= sub_movement.ogg
#FLAG= 1
#TYPE= 2
#AI= 0
#LEVEL= 0
#GV= 1[1,100]
#LINK= 0[0]
#COUNTRY_ID= 45
#ALIGNMENT_ID= 0
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; should be changed to:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
#COUNTRY_ID= 0
#ALIGNMENT_ID= 1
#FLAG_ID= 21
#TRIGGER= 100
#SEASON_FLAG= 0
#DATE= 1939/09/01
#SOURCE_POSITION= 29,96 [-1.6]
#SOURCE_POSITION= 30,97 [-1.6]
#SOURCE_POSITION= 31,96 [-1.6]
#DESTINATION_RESOURCE= 30,95 [1,2]
#DESTINATION_RESOURCE= 29,92 [1,2]
; 1st Line - Germany(45) politically aligned with Axis and not surrendered
; 2nd Line - Canada(21) politically aligned with Allies and not surrendered
#VARIABLE_CONDITION= 45 [1] [100] [0]
#VARIABLE_CONDITION= 21 [2] [100] [0]
}