Degrees from same school but different departments?

[Matt W.]

I was wondering what the general perceptions are for getting all three degrees from the same school, but in different departments (and therefore different faculty and methodologies). My rundown is thus: I got my BA in one department, left for a year to pursue something else, then returned to the same school in a related, but entirely separate, discipline. I am currently faced with the option of continuing on at the same school for the PhD in the same program as my MA, but I am concerned about the stigma of "academic inbreeding" and what effects this may have. I know this is an issue for the same degree, but I don't know what the perception is for going to the same school but for two separate disciplines. Any thoughts would be welcome.