So I've ran through this reaction several times and every time my yields are much lower than I've seen reported.  Let me run through my procedure..

Peracetic
This is basically Chromic's procedure, but with less DCM.  I've read reports that the large amount of DCM used in this reaction is only used to keep reaction rate/temps down.  I drip my DCM/iso in very slowly, with the reaction flask on an ice bath.  It never reaches reflux, despite the reduced DCM:iso ratio.  I stir for at least 16 hours, separate the oil, extract aqueous with DCM, combine extract with oil, then wash several times with dH2O.  The apparent yield from this procedure is pretty high....if I put in 50g isosafrole, I can get up to 55g oil out of it.  Of course I don't know how pure this portion is, but it SEEMS like the reaction goes well.

Pinacol
I think this may be where my yields are being killed.  I follow this procedure:

From the extracts from a peracid rxn containing .3mol isosaffy (48.6g), the glycol is added to: 75mL MeOH, 125ml H2O then 125ml 31.25% HCl. The mixture is refluxed 2.5 hours, the oil drained from the bottom of a sep funnel and further extracted 3x60ml DCM. The ketone distilled and at least an 80% yield can be had..

But generally go for more than 2.5 hours because I live at altitude and the reaction takes place at a lower temp.  Once finished, I separate. extract aq. with DCM, combine extract and oil.  Then I wash with water, several times with bicarb, then brine.  I back extract the water washes with DCM, then wash the back extract with bicarb and brine.  Evaporation of the DCM yields a tan-colored oil.

This is then distilled under vacuum.  MDP2P comes over a nice clean fluorescent yellow color, but only in low yields.  Last run was 20g from 73g glycol.  Once the MDP2P comes over I'm left with a large amount of viscous brown oil in the reaction flask that, upon cooling, becomes mostly solid.  Roughly the consistency of a starburst candy.

I can't figure out where this brown oil is coming from. 

Any ideas?

Yes, I am doing the buffered peracetic.  And I didn't mention it, but I am backwashing the epoxide water wash.

As for TLC, I vaguely recall someone doing it with regular filter paper.  I'll look into that.

I suppose the peroxide could be going bad, but I'm using it between 7-10 days after mixing.  It goes into the freezer after 7 days.  I don't have any easy way to figure out what percentage it is.

My vacuum goes pretty low...distills safrole at <100C, so I don't think that's the problem.