It's because in js, number literals prepended with 0 are considered octal (base 8)
For example
010 == 8
In your example 040000 is really 4*8*8*8*8 = 16384 because in octal each 0 in the right multiplies the value by 8.
EDIT: Bonus:
If the leading 0 is in a string representation, (for example, if it was introduced by the user), and you want to avoid converting to octal, specify the base (aka radix) with value 10 in the parseInt method call, like this
var number = parseInt("040000", 10); //number will be 40000 ;)
In recent browsers, the radix is 10 by default, but not in old browsers, so if you want maximum compatibility also, always specify the radix parameter (usually 10).
Cheers