I made the mistake of buying the ADMS (Yaesu/Vertex) version of the programming software. It was a piece of junk and didn't work.
The RT Systems software (ARDTS 7100) is superior, but still clunky. At least it works, sort of.
Here's the deal. If you modify your radio to TX out of band, ie you've removed one or more of the initialization diodes/jumpers, your radio is now "different" than it was before. Consider it a personality change. The old files you had won't work.
To make it work, you have to DOWNLOAD to a new, empty freq file, make entries into *that* freq file, then try uploading the new freq file to the rig. It's catch-as catch-can with any of these programming softwares, for me most of the time it doesn't sync up very well at all.
BTW, if you do buy from RT, ensure they send you the software on CD, not floppy. I bought the programming pkg (software and cable) for the FT90/FT2600 at the same time as the 7100 ware. The software came on diskette. It was an old version, and wouldn't install. I emailed RT Systems, and about 2 weeks later, Karin sent the newer version on CD. I discovered the cable was the wrong one too the first time the software actually fired up, it wouldn't talk to the radio.
To RT Systems' (Karin Thompson, the programmer) credit, they will fedex you replacements no questions asked. Just make sure you either call them, or email them during the hours they look at email: Tuesday, Wednesday, or Thursday, from 6 to 9 PM eastern time.