I don't remember ever running into this issue before (V3.1). I go into supports, click on automatically generate supports, then click on Remove Support Structure and remove the support structure that I do not want. Everything looks good, until I hit Prepare to print button and the print preview display the supports that were supposed to be removed.
Just because the software doesn't behave the way you believe it should, it doesn't mean there's a bug!
The way to manually adjust the generated support is as follows:
1) Set the support to auto-generate support....but set the resolution to a high value so that no support can be generated.
2) Open the support generation pane
3) Set the parameters for auto-generation of support using a realistic pillar resolution.
4) Hit the Generate auto support button...this generates the basic support
5) Use the tool to remove and/or add support as required, setting the pillar resolution to add support at the required resolution
6) When you're happy, exit the pane.
When you slice the model, as the auto-generation pillar resolution is set too high for meaningful support to be generated, none will be created....and the support you want, and only the support you want, will exist. This all works...no bugs!
I'm not sure what usage instructions you're referring to, but they have tutorials on their website and videos that explain exactly how this stuff works, and it's doing exactly what it should.
If you enable support generation, then it's going to make sure you have support for you model. If you place some manually before you slice, then it knows not to add automatic support since you already added some. However, if you don't add any support and you still have support generation enabled, then it's going to add support automatically. That's how it's always worked.
And this works model-by-model. So if you add manual support for just 1 model, it may still add automatic support for the second model if your process for both of them has support generation enabled.
I am referring to this tutorial https://www.simplify3d.com/support/tuto ... tructures/. I don't see anywhere in it's instructions that alludes to or indicates that removed support structures will be generated anyway which is in fact what is happening. It seems to say just the opposite.
To be clear, there is a different between "I removed some supports" and "I removed all of the supports for my entire model". As it says, if you enable support generation, it's going to make sure that there is SOME support for the model. The only way to stop that is to either add your own supports manually or disable support generation all together. So if you are trying to stop support from being added, then just disable support generation.
If you're still having trouble, post your factory file and explain exactly what steps you are taking.