Unfortunately, it appears that the employee has developed a "victim mentality." This root of this mindset is trust issues, and they're not unwarranted. Try to understand that this is a normal reaction from a member of a suspect class that has traditionally been on the receiving end of discrimination and oppression, both overt and subtle. Some minority employees are better than others at filtering out "everyday" personality clashes and actual discriminatory behavior than others.

As I see it, since she is an otherwise productive and valuable employee and it seems by your tone that you wish to keep her on, your only option is meticulous recordkeeping and investigating all claims of harassment or discrimination thoroughly. You can be sure that if you ever have cause to fire this employee, you will find yourself the Defendant in an EEOC action. The outcome will most certainly be favorable to your organization if copious notes are kept.

I would also recommend a thorough harassment training be conducted with all employees, and make up a couple of similar scenarios to demonstrate more what is and what is not harassment.

In addition to prior postings (all to which I agree), I would consider seeking feedback from a trusted, yet, external source (if you have not already done so). And yes, although we consider ourselves objective professionals (HR), what I have observed is that although all good and equal intentions are meant, some of what seems like "an overreaction" could be "valid".

This gesture will also demonstrate to the length for which the company has gone since there are repeat concerns brought to HR's attention.