I support the old part system as much as I can but converters are not perfect. I may find better algorithms later, and/or textures will be converted at some stage.

Improved. It is much better now.

I'm finding issues with transparency as well. Many parts don't change at all when a transparent color is chosen, and even pieces with a transparent preview image will be added to the workshop as a solid color.

A new system of dealing with decorated parts was recently implemented into Mecabricks. As Scrubs said before, he supports parts using the old system as much as he can, but not everything is able to be made perfect.

Just to clarify, are you saying that parts must each be manually updated one by one to work with the new system?

Yes, and it is a time-consuming process for Scrubs.

I don't doubt it takes a lot of work. I'd be happy to help if there was a way to easily pass off tedious tasks to a group of people.

One suggestion is the possibility of immediate feedback (dialogue box pop up, etc) when coming in contact to something of this nature (like new vs old parts situation), so users would know that something wasn't yet supported. It this point it fails silently which is hard to troubleshoot. This would help to parse out what is a bug vs. just a feature issue, and may minimize bug reports.

I agree, that would definitely be something useful, although this is only a temporary problem which probably doesn't justify coding a whole new feature.

I'm glad to know I'm not the only one with this issue. For now, is this issue only in the design window or does it carry through to rendering as well? I know that the transparent parts that I loaded in that appear solid DO render properly as transparent but if I try to change a part color will that also carry through?

Thank you!

Converter is different in Blender and Mecabricks (as both systems are different). So sometimes something that doesn't work in Mecabricks may work in Blender (and vice versa). However, if it is an old decorated element that is not following the current rule, it is likely to not work in both. Which one is the issue for you?

I don't personally use the Blender add-on. I only render through your render farm here so I can only speak to that. I do need to edit my comment above however, as it seems that some of the "transparent" parts that aren't showing up as transparent in a final render either. So far I have noticed these mostly with the stickered elements in the Ninjago City sets. I expect that is just the issue you mentioned above that not all parts have been transitioned over properly.

The online render mode is based on Blender and the code for the converter is similar.
Decorations and parts are moved to the new part system which will remove over time all these issues as image processing old textures won't be needed anymore. However it will probably take years to fully complete this task. This is a manual process. Each mesh and each decoration will have to be manually updated. It is about 3,500 meshes and 15,000 decorations that have to be transferred! 1000s of them have already been processed by admins.
Do you have a specific item that I could look (mecabricks ID)?

Aye, I do have a few parts that I was hoping to use fairly soon. The three main ones that render as opaque but shouldn't are 30292d6, d7, d8. 18675d4 shows up as opaque in the editor but DOES end up rendering properly as transparent. However, I am likely going to be working on my own custom textures to use instead and I have a number of good alternatives to those parts so I should be able to get along more then well enough. That is a crazy amount of work that you all are putting in, we all really appreciate it!