I've used the FT-60R Commander software quite extensively, and I've never had a problem with DCS codes. Granted I only have a handful of frequencies that use DCS compared to the the dozens that use CTCSS, but none have ever just disappeared.
Have you tried to contact Jim directly? I had to do that once quite a while ago with, I think, a VX-2R Commander problem. He was very quick to get back to me and fixed the issue within a couple weeks.