Yup.. sure am. I found that out when I was chosing which vendor to use for a 50 AP rollout...
It REALLY gave me the craps.
The reason is that PEAP is EAP within EAP and both Cisco and MS use different forms for the 2nd level EAP exchange. (MS uses MS-CHAP v2 and Cisco uses... ? not 100% sure)
You really have 2 choices at the moment (but there is a resolution in the wind that I'll get to in a second)
 Use the ACU on the clients and a CiscoSecure ACS server
 Use only windows 2000/XP clients and you can use MS IAS server
The resolution in the wind in the new version of the Cisco ACU which will support PEAP for MS IAS.