H4s are intentionally using small caps. The issue I’m seeing is not that the numbers are a different size, but that I had accidentally set the headings to be all lowercase. If you download the latest version this is fixed.
If you want to switch from small caps to all caps you can uppercase the H4s like so:
.markdown-preview-view h4, .HyperMD-header-4, .cm-header-4 {
text-transform: uppercase;
}