Vmmaker will clear all modelines in registry, not sure about Soft-15kHz though, but as long as you can confirm Taito games working, it'll be worth to check the registry.
BTW it's not the first time this issue has been reported, but I never tested it myself. It's Taito games's fault however not having proper setup options to unambiguously target a certain mode.
I'm thinking it may be interesting too to check Arcade OSD in both situations, specifically which modes are reported in each case.