There is no doubt that there are differences between Jaap Sahib in different Gutkas. If you have access to a Gutka Sahib published by Master Jaswant Singh jee, it would be a good idea to use it to write Gurbani. Master jee did quite bit of research before publishing them.
Having said that, for the purpose of writing Gurbani, we know that despite differences, 95% of Gutkas are same. The Mahaatam of writing would not be diminished due to minor differences.
With Maharaj jee's kirpa a lot of Gursikhs out here in the West, especially the youth, is turning towards writing Gurbani. This is a wonderful development. Guru Sahib kirpa karan.
Daas,
Kulbir Singh