I re-read my question and realized I made a confusing one, so I am rewording a LOT.
So the software I use is Craftware. When it comes to the first layer I have it set to .25mm, with the following layers being whatever I specify otherwise. And because of this there shouldn't be a difference with the first layer even though I choose different layer heights based on the project. But for some reason it is not the case.
When printing .2mm layer height everything works great. The print adheres amazing, the nozzle is at a really good height. Everything simply works.
When printing .1mm the first layer does not stick. A lot less plastic is coming out the nozzle. And it is a disaster. Have tried increasing the amount of flow a bit, but didn't help (I might need to raise it a lot more)
So I don't understand what is going wrong. The first layer is supposed to be set at .25mm no matter what the layer height is otherwise. What do I need to do or look at?