<p>I re-read my question and realized I made a confusing one, so I am rewording a LOT.</p>

<p>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. </p>

<p>When printing .2mm layer height everything works great. The print adheres amazing, the nozzle is at a really good height. Everything simply works. </p>

<p>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)</p>

<p>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? </p>

You have asked several questions here.
"why is first layer set to 0.25" -- check the gcode file, opening it in a text editor, to see what layer values are specified.
"looks like under-extrude" -- please show a picture.  If it's purely that the print failing to adhere, you may need to adjust the Z-zero point slightly. Or perhaps When you printed at 0.2mm, for whatever reason the transverse stress on the base layer is less than when printing at 0.1 mm (e.g., linear speed adjustments needed).
Is the second layer somehow not adhering to the first layer?  It is possible that the linear speed setting for the first layer is too high and that should be adjusted.  Or perhaps the z-height for the second layer is inconsistent with a 0.1mm layer setting, so check the gcode there too.
In general, adherence problems can be dealt with by adding a raft or brim. See if that suffices.