After first layer temperatures not being generated in gcode

I'm posting this here to get some feedback before reporting it on github.

I’m going to try and make this as simple as possible to understand. If I confuse you (likely since i confuse myself) just ask and I'll try and explain it better

I am currently using Repetier Host/FW, and Slic3r 0.9.3

I have my printer setup so that Slic3r handles all temp settings (Bed & Extruder). I like to have my machine do the following when I click "Run Job"... (my start gcode is at bottom)

1. Home X,Y,Z (this puts my nozzle on the bed so it doesn’t ooze)
2. Set first layer bed and extruder temp and wait
3. Prime extruder
4. Print first layer
5. Change to Normal (second layer –to- last) temps (Bed & Extruder)
6. Finish print

the only way I have found to do this is to set in slic3r:
-Filament settings
--Filament
---Temperature = 220
---First layer temperature = 0
---Bed Temperature = 110
---First layer Bed Temperature = 0
If I use First layer settings it puts them above my "home XYZ" in Custom Gcode

My Custom Gcode for start is:
G28 ; Home all axes
M104 S224 ; Set nozzle temp, no wait. -gets things heated up at same time
M190 S114 ; Set bed temp, wait.
M109 S224 ; Set nozzle temp, wait.
G92 E0 ; Reset extruder
G1 E3 F1200 ; Prime extruder 3mm
G1 E2 F1200 ; Retract extruder 1mm
G92 E0 ; Reset extruder

The problem is when the gcode is generated after the first layer there is "M104 S220 ; set temperature" for the extruder but nothing for the bed.. If this is a known bug just let me know so I don’t report it on git, I looked but might have missed it.

Answer was given in [github.com]