That's probably due to the monitor preset you're using. VMMaker doesn't support CVT but it supports VESA GTF (similar, older).
There are several VESA presets in the monitor preset dropdown menu, pick the one that has the maximum number of lines you want to use, e.g. vesa_800 allows up to 800p resolutions, etc.
You don't to add your desktop resolution to the user's mode list. That's a PC monitor, so that resolution it's already provided by its EDID to Windows, you don't need to override it with a calculated modeline.
Then, you say you previously did 3840x240@60Hz using CVT timings. How was that? Does your monitor support 15 kHz? Was that doublescanned?