Under some conditions, no skyline shift is applied, e.g. too few lines (<5), high RMS in fit (>0.4 pixels), short exposure (<420s), or a high RMS/shift ratio (>4). These conditions are noted in the makee output log.
The shift used is recorded in the FITS header as "SKYSHIFT", see also "SKYSHMEA" for the measured sky shift, "SKYSHRMS" for the RMS in the fit, and "SKYSHNPT" for the number of points (lines) used.
You can look at the plot file to see if the shift (or lack of shift) is appropriate. You can override the value (or lack of value) using on the makee command line using the "-noskyshift" or "skyshift=" options.