I administer COBRA in-house for my company of 2,500 employees. I have about 20 active COBRA participants. I am having a lot of problems with my "Benenfit Plans System" software. Does anyone know a good software for adminisering COBRA?

Try COBRA Administrative Manager by COBRA Solutions.
http://www.cobra-solutions.com/products/cobra.htm
It used to provide a COBRA tracking and notification software program on West's Compensation and Benefits Advisor CD-ROM.
I do not know the current status of the West product. I believe the above Website may provide some information about the COBRA Solutions software.
Several of the providers of other benefits software programs also offer COBRA-related products.

You may want to also try TRAVIS. They have a great system that is pretty easy to use. I think they are based out of Texas.

Good luck.