Ok, so I messed around trying to figure out why, then tested the the bug I discovered.
First; running the latest Version of S3D V5.0.1
<Starting Script BUG>
So I Like the feature, just not the bug, lol
<A>
If you do not put any variations of extruder temp variable in the Starting Script, even if it committed ';" out, you will get the following as expected. So bed the extruder temperatures added automatically at the top of the gcode fie.
<In Starting Script>
; no temperature veritables used i.e. [extruder0_temperature]
</In Starting Script>
You Get:
<gCode Output>
M140 S65
M190 S65
M104 S225 T0
M109 S225 T0
</gCode Output>
</A>
<B>
If you add the following to the Starting Script, and it surprised me that is was there. It makes it so you do not have to replace the tool temperatures at the top of the gCode.
<In Starting Script>
G29 L35 R270 F20 B260 V4 ; Bed Leveling (Bilinear)
G1 X5 Y5
G1 Z0.3
M104 S[extruder0_temperature]
M109 S[extruder0_temperature]
M117 Printing...; Display Printing to Dispaly
</In Starting Script>
You Get at the top of the gCode that Simplify3D puts there as desired:
<gCode Output>
M140 S65
M190 S65
</gCode Output>
From your Starting Script as desired:
<gCode Output>
G29 L35 R270 F20 B260 V4 ; Bed Leveling (Bilinear)
G1 X5 Y5
G1 Z0.3
M104 S225
M109 S225
M117 Printing...; Display Printing to Dispaly
</gCode Output>
</B>
<C>
Even if you commit ";" out them, it still behaves as if they were not, but will treated them as they are committed out when executing them as they are committed out. It is my opinion this logically should not be the case.
<In Starting Script>
G29 L35 R270 F20 B260 V4 ; Bed Leveling (Bilinear)
G1 X5 Y5
G1 Z0.3
;M104 S[extruder0_temperature]
;M109 S[extruder0_temperature]
M117 Printing...; Display Printing to Dispaly
</In Starting Script>
You Get at the top of the gCode that Simplify3D puts there NOT as desired:
<gCode Output>
M140 S65
M190 S65
</gCode Output>
From your Starting Script as desired:
<gCode Output>
G29 L35 R270 F20 B260 V4 ; Bed Leveling (Bilinear)
G1 X5 Y5
G1 Z0.3
M117 Printing...; Display Printing to Dispaly
</gCode Output>
<Starting Script BUG>
</C>
<Post-Processing BUG>
If you put his in your Post Processing it will work, but the color coding get confused when you add a commit ';' in any of the "Search" or "Replace" Strings.
<Post Processing>
;AUTO-PARK MODE.
{REPLACE "G90\nM82\n" "G90\nM82\nG28 X\nM605 S0; Enable Full-Control Mode (Resets mode state.)\nM605 S1; Enable Auto-Park Mode\n"}
</Post Processing>
Everything after \nM605 S0 is green like it is a commit, but still produces the desired outcome (See Picture Attachments).
<gCode Output>
G90
M82
G28 X
M605 S0; Enable Full-Control Mode (Resets mode state.)
M605 S1; Enable Auto-Park Mode
</gCode Output>
</Post-Processing BUG>