Navigate to where you’ve installed Inkscape (for me, this is C:\Program Files (x86)\Inkscape), then open the share folder, then open the ui folder. The folder you should be in is C:\Program Files (x86)\Inkscape\share\ui and you should see a file called units.xml.

Make a copy of units.xml called units.bak.xml and then open the original units.xml in a text editor.

Change your file from

    %
    %
    %
    1.00
    Percentage


    pixel
    pixels
    px
    1.00
    CSS Pixels (90/inch)


    point
    points
    pt
    1.25
    PostScript points (72/inch)


    pica
    picas
    pc
    15.0
    12 points


    inch
    inches
    in
    90.0
    Inches (90 px/in)


    millimeter
    millimeters
    mm
    3.543307086614174
    Millimeters (25.4 mm/in)


    centimeter
    centimeters
    cm
    35.43307086614174
    Centimeters (10 mm/cm)


    meter
    meters
    m
    3543.307086614174
    Meters (100 cm/m)


    foot
    feet
    ft
    1080
    Feet (12 in/ft)


    degree
    degrees
    Γö¼Γûæ
    1.00
    Degrees


    radian
    radians
    rad
    57.29577951308232
    Radians (180/pi deg/rad)


    gradian
    gradians
    grad
    0.9
    Gradians (360/400 deg/grad)


    turn
    turns
    turn
    360
    Turns (360 deg/turn)


    font-height
    font-heights
    em
    1.00
    Font height


    x-height
    x-heights
    ex
    0.50
    Height of letter 'x'


    half-em
    half-ems
    en
    0.50
    Half of font height

to

    %
    %
    %
    1.00
    Percentage


    pixel
    pixels
    px
    1.00
    CSS Pixels (72/inch)


    point
    points
    pt
    1.00
    PostScript points (72/inch)


    pica
    picas
    pc
    12.0
    12 points


    inch
    inches
    in
    72.0
    Inches (72 px/in)


    millimeter
    millimeters
    mm
    2.834645669291339
    Millimeters (25.4 mm/in)


    centimeter
    centimeters
    cm
    28.34645669291339
    Centimeters (10 mm/cm)


    meter
    meters
    m
    2834.645669291339
    Meters (100 cm/m)


    foot
    feet
    ft
    864
    Feet (12 in/ft)


    degree
    degrees
    Γö¼Γûæ
    1.00
    Degrees


    radian
    radians
    rad
    57.29577951308232
    Radians (180/pi deg/rad)


    gradian
    gradians
    grad
    0.9
    Gradians (360/400 deg/grad)


    turn
    turns
    turn
    360
    Turns (360 deg/turn)


    font-height
    font-heights
    em
    1.00
    Font height


    x-height
    x-heights
    ex
    0.50
    Height of letter 'x'


    half-em
    half-ems
    en
    0.50
    Half of font height

All of your units now will calculate correctly! As a test, create a box with size 72px by 72px. Changing the units afterward, you’ll see that this is equal to 1in and correct for the other values as well.

Make sure you also set your default bitmap resolution to 72dpi in Preferences (Shift + Ctrl + P) -> Bitmaps

Another cool feature is that Inkscape supports em units! However, after reviewing the source, the base font size is fixed at 12px. Maybe I can submit a fix for this, hmm.

Happy Inkscaping!