ok well, 2 things then... make sure you are only loading files with the suffix _c_d_r.xisf or _c_r.xisf into ImageIntegration. by default those are the filename suffixes that get applied by Calibration, Debayer and StarAlignment. since you want to integrate the registered images, the input files to ImageIntegration should always end with _r ("registered").
if StarAlignment is unable to register some of your images, there are usually 2 problems. with uncalibrated images, there may be a lot of hot pixels in the image and SA mistakenly identifies those as stars. in some cases it aligns all the images to the hot pixels, which means that the _c_d_r or _c_r output files are actually unregistered. the way to fix this problem is to increase the noise scales and the hot pixel detection controls in StarAllignment. another problem commonly seen is that the stars are too soft or too elongated and StarAlignment does not detect them. there are also sliders in SA to be more forgiving when detecting stars. in this case SA will fail to register the files and will not output a _c_d_r or _c_r file at all.
rob