There's no HIMEM/EMM386 in DOS 3.30, so Checkit has to control the protected mode on its own.
I guess you're using DOS 6.20 with HIMEM (and maybe EMM386 as well), so Checkit makes use of them to access the protected mode.
Try running 6.20 with empty CONFIG.SYS and AUTOEXEC.BAT...
I think it's some incompatibility with Checkit, I also encountered similar problem with some machine, but forgot any details...
Anyway, if stuff like HIMEM, EMM386, Windows 3.x in Standard and Enhanced modes works fine, then there's nothing to worry about.
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