Are there different accounting treatments for HSA's and HRA's?

Yes, HSA's and HRA's must be handled differently.

HRA’s are employer-funded plans, and as such, are considered general assets of the company. These plans reimburse employees for incurred medical expenses that are not covered by the standard insurance plan. All distributions made from the plan are considered tax deductible to the employer, and are generally tax free to the employee.

HSA's are employee-funded plans, though they can also be funded by employers or third parties. HSA’s are either trust or custodial accounts. Employee’s contributions to their account are tax deductible, as are any contributions employer’s make to an employee’s account. Any distributions from the plan for qualified expenses are tax free, but any other distributions are taxed as income with a 10% penalty (with a few exceptions). HAS’s tend to be more complicated, especially when funded by multiple sources.