I'm using TT Deluxe Desktop and am having the same problem. It's not the refund amount that's the issue, it's that TT is transferring radically wrong numbers from my old return to my 1040-X. Like others on this thread, it looks like I will have no alternative but to prepare a 1040X by hand and file my amended return by mail.
I called TT support. The guy I talked to was a nice guy but provided no help at all. From searching this forum it appears that this issue is several years old but apparently is receiving no attention at all from TT.
