This is a limitation of legacy fonts. You may need to type the consonant first, then the vowel sign. For example, to type 'કિ' (ki): Type K (ક) then I (િ). If it still fails, use a dedicated keyboard driver like "Gujarati Indic IME" turned OFF.
Using the layout, type the following English keystrokes: kA ir Zn uH gm fU j hari krishna gujarati font keyboard layout pdf
The most confusing part of the Hari Krishna layout involves vowel signs (matras) and conjuncts. For example: This is a limitation of legacy fonts