Well, i did call irs today and the problem is solved but this is i found.
The return was filed MFJ but the CP59 was issued to wife as she did not file the tax return for 2008. The name and SS# were correct on the copy of the tax return. The person who did data entry at IRS missed to mark that return is MFJ (some check mark in front of wife name). So IRS computer recognize the husband did file but wife is missing.
When i gave all the info over the phone, they saw the problem at there end and transfered me to the second lever who can fix this check mark error done by IRS. Finally got the live person and he took care of it.
The second level CSR told me it is done & no more letter coming from IRS. I requested to mail client a confirmation letter so client has some record. The CSR denied that there is no such letter and problem is taken care of so why to worry. I insisted more and finally agree to send one. I am just crossing my fingers that client may get a confirmation letter and no more CP59.
Client was with me for whole 51 minutes and now he agrees that he will EFILE from next year.
Thank you for all your input.