Did you try FracPad on a (Windows/Mac) computer? That should allow LFO B Phase modifier assignment. I used it for that while borrowing an Axe III a few months ago.
Your details of the Virtual Toggle testing don't seem to agree with the release notes. I'm assuming when it took 4 presses to toggle, you tried 4 more presses to verify it wasn't just getting in sync and then toggling every other press.
If it kept requiring 4 presses, this might be programmed or documented incorrectly rather than a setup issue. It sounds like the ratio should be 2:1 at most, for a latching switch with "Virtual Toggle" selected. https://forum.fractalaudio.com/threads/fc-features-notes-for-firmware-5-07.150309/
Your details of the Virtual Toggle testing don't seem to agree with the release notes. I'm assuming when it took 4 presses to toggle, you tried 4 more presses to verify it wasn't just getting in sync and then toggling every other press.
If it kept requiring 4 presses, this might be programmed or documented incorrectly rather than a setup issue. It sounds like the ratio should be 2:1 at most, for a latching switch with "Virtual Toggle" selected. https://forum.fractalaudio.com/threads/fc-features-notes-for-firmware-5-07.150309/