Currently skew transform uses tangent values. I learnt this only from http://forum.high-logic.com:9080/t/the-skew-facility-of-the-glyph-transformer/3210/2 Neither the user interface nor the documentation explains this. (Sorry if I missed out seeing anything.)
Angles are more naturally understandable than tangent values. Inkscape uses angles for the skew transform.
Please change the skew transform tool (whether in Transform toolbox or in Glyph Transformer wizard) to use angles and not tangent values.