I thought that by using ';' then I would be able to stop the program from loading the individiual settings.
However, after a complete re-boot, I have all the icons back again.

e.g.
[TrayStatus Settings]

;Show the Num Lock icon
;NumLock=1

;Show the Caps Lock icon
CapsLock=1

;Show the Scroll Lock icon
;ScrollLock=1

;Show the HD activity icon
;HDActivity=1

;Minimum bytes/sec read to trigger icon
HDActivityRead=50000

;Minimum bytes/sec write to trigger icon
HDActivityWrite=50000