If you are doing "ratio to heavy", you need to make sure that your "Blank" replicates do have the heavy standard spiked into them.
If a replicate did not have any heavy standard in it, the numbers that get plotted on the calibration curve would essentially be random numbers (noise divided by noise), and you would not get the results that you wanted.
If a sample contains neither heavy nor light material, it should be called "Double Blank", and it will not be used for the LOD calculation.
It is certainly possible to have a LOD which is higher than the LOQ.
The LOD and LOQ are calculated in very different ways, and Skyline does not do anything to prevent one number from being higher than the other.
If you still have questions, you can send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you an attach it to this support request. Otherwise you can upload it here: