Well... looking at the numbers that are used, you might take a hint from their magnitude: they are really big numbers. The equivalent script using decimal numbers would look like this:
var n = 18014398509481984;
var m = 18014398509481986;
var eq = (m == n);
The puzzle script with decimal-encoded numbers. Yes... eq == true what's up?
Yes, the numbers are big... but not so big they won't fit in a 64-bit integer. Looking back at the previous post's script, notice that the bigger of the two numbers is 0x0040000000000002; the largest 64-bit integer would be expressed as all sixteen hex digits with a value of F. It's not a sign issue, since the MSB of isn't set for either number.
So JScript must be storing the numbers internally using something other than a 64-bit integer to store the values. In fact, it uses the VARIANT data type. A VARIANT is a discriminated union that can hold just about any common data type--very useful for 'typeless' languages like JScript. A modern (post-Windows 2000) VARIANT can hold a 64-bit integer (a.k.a long long, or VT_I8 in VARIANT-speak), but JScript 5.6 doesn't use it, probably for legacy compatibility reasons.
So now, another puzzle: what VARIANT type does JScript use to hold these large integers? (hint: it's not VT_I4!)