I failed a crucial course for my major that serves as the foundation for many other core courses.
This by itself shouldn't prevent you from attending grad-school. Good students fail courses sometimes for a number of reasons, family emergency, taking too many classes, working too many hours at a job, etc.
and have kept straight A's in my upper-level courses since then. [...] this is a potential deal-breaker
I feel there is more to this situation than a single failed class. Is your GPA in line with the published average of an accepted grad student? Were you a middling freshman student, and got serious as a Junior? Does your transcript bear out that this one class was a fluke, or does it show a return to an old pattern?
If you have a good overall GPA, and good letters of recommendation, then I don't see why an admissions committee would dwell on a failed and re-taken class.
By "graduate admission committees" did you do an interview with the faculty members of the department in which you will be working? In general, you submit your application to the university, which then filters base on minimum GPA and test scores, and passes it onto the department you applied to. Did you talk with someone in the department you'd like to attend, or a person in the admissions department?