There is no correlation between the FK and a creation of an index. When creating the index, FK constraints need not to be checked, they were checked either when constraint was created or when the data was inserted/updated.
So how can it be that index on one column takes a couple of minutes, while index creation on on another column of the same table can take an hour? It depends on many things. For example, the majority of values in the first index column might be null (nulls are not included in regular B*tree indexes), while in the second index column there might be "not null" constraint. Or the selectivity of the column of the first index is very low, while in the second index's column it is high, hence spending much more time on performing sorting.
Setting the larger sort_area_size mighd speed up the index creation process significantly, this would be my first shot.
Jurij Modic ASCII a stupid question, get a stupid ANSI
24 hours in a day .... 24 beer in a case .... coincidence?