Ok, what happens here is that the scale factor on the base mesh ends up wrong by a factor of ten. This is also the reason why you need to apply the target ten times to achieve full effect.
The reason the scale ends up wrong is because the UI setting for scale mode isn't available. And the reason for that is that this is a setting from MPFB1, which I'm guessing you're not using.
So, a chain of bugs. I'll see to fixing MakeTarget standalone so that it is compatible with MPFB2, although I think that in the longer run it might be better to retire the standalone MakeTarget altogether since there is a more up to date version included in MPFB2.
Anyway, my primary suggestion to solve your problem is this:
* Install MPFB2 if you have not already done so. If you're unfamiliar with it, see quick start instructions on
http://static.makehumancommunity.org/mp ... arted.html* Rename the shape key to "PrimaryTarget" (see screenshot below)
* Use the version of MakeTarget included in MPFB2 to save the target.
Having used this approach, the target looks sensible in MH.
Alternatively, you can wait a day for me to fix the bug in the standalone MakeTarget.
As a side note, you would also need to modify the helper geometry in order for the eyes to follow. Unfortunately, this geometry seems to be deleted on the base mesh in your blend file.