I managed to figure it out, I was having plugins loaded the wrong way.  
They were being loaded as json tiddlers after the command started rather 
than being placed in the plugin folder beforehand.  I think that meant when 
I was running the commands, they weren't getting picked up, but once the 
html file was generated, next time I went to save, they were found.

On Saturday, September 14, 2019 at 3:41:58 AM UTC-4, TonyM wrote:
>
> Mathew,
>
> I doubt I have the answer, but are you aware the raw tiddlers are handled 
> differently during save, they are placed in a different place in the 
> wikifile to be active as a result of where they are placed in the wiki html 
> file. Take an empty.html add a raw tiddler with content and open the html 
> file in a text editor and you will see what I mean.
>
> I expect this could throw light on your observations.
>
> Regards
> Tony
>
> On Friday, September 13, 2019 at 10:39:50 PM UTC+10, Matthew Lauber wrote:
>>
>> All, I'm running into a strange issue with the $:/tags/RawMarkup tag.  
>> I've got some html element definitions I need to put in the start as raw 
>> html.  I used the $:/tags/RawMarkup tag, and it works great.  Not a 
>> problem, see attached testing.html.  
>>
>> However, when I try to use the same plugin with the same templates on 
>> github, I run into a strange issue.  I render the html file via the 
>> --rendertiddlers command and the rawMarkup isn't present.  (Look at the 
>> "D&D Creature Manager" plugin on https://mklauber.github.io/tw5-plugins/).  
>> But if I tell that page to save to file, it works again.  
>>
>> I'm not sure exactly what could be going on here.  I'm using travis-ci to 
>> automatically build the index.html file, via the travis.yaml and 
>> tiddlywiki,info files here: https://github.com/mklauber/tw5-plugins/ .  
>> But I can't think of anything I could be doing wrong that would prevent 
>> tiddlywiki from rendering the rawMarkup, unless it doesn't check the 
>> external plugin files for $:/tags/RawMarkup?
>>
>> You can see the travis-ci logs here: 
>> https://travis-ci.org/mklauber/tw5-plugins
>>
>>

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