Steven,
the transp IT8 target you're using 'could' have been drifting a little
bit from what the reference/descriptionfiles tells in numbers for
targetvalues. Aging of the target or a massproduction of targets will
always show "offs". They're not measured individually or they are VERY
expensive.
Scanning the lightsource itself and not through the clear filmbase
is giving you light levels above what is profiled. The filmbase will
always steal light and is profiled as white a bit lower than the empty
slideholder. Variations can be found there maybe. If you're scanning a
clear slide it could be tinted as someone else mentioned here. Tinted
in another way than the target. If the readings are the same on
filmbase as is in empty slideholder, I would expect the drifting
ref-file>IT8 target beeing a thing here.
A part from that, when building *scanner*-profiles with Profilemaker
Pro or Monaco Platinum I do see differences inbetween these softwares
themselves and I do also see that non is really totaly perfect in
greyramp when reading numbers. How could it be possible that a simple
utility like Vuescan IT8 or the freestanding brother of it, would
deliver better than these industrystandard apps? Well, it could be if
you're a lucky guy but you don't seem to be that for the moment.

We
would have to read the IT8 target with a Spectro and compare the
measurefile in Profilemaker with the ICC profile from Vuescan, to get
delta-E values. To see how much Vuescan fails when reading the IT8 and
by that understand what our eyes will se or not of it based on these
delta values.
Also, let Vuescan deliver a scan from the profiled settings **in the
profiled space** (if possible) and in Photoshop make conversions from
that into your workingspace with different renderings (perc vsv relC).
That could make a difference of what you start working with for the
editingpart...and I think that is what counts. We do avoid editing in
the scannerpace as is. This space is not greyballanced like a
workingspace like Adobe RGB or Colormatch RGB.
Diffrent CMS engines are known to deliver differently...so letting
Photoshops engine do the conversion may deliver something else than
what Vuescan-conversions gives you on the fly.
nikita