Trying to get some new single pack varnish onto some existing varnish, and it looks like its been spotted with silicone - the varnish 'retreats' from certain areas if you know what I mean!
Presume its all of these lubricating sprays and sealants used more commonly now.

Anyone know of a magic liquid or process to make sure the contaminants has been removed? Thinners and sanding? Acetone? Burning (joke)

You'll need to get the new coat off first.
Acetone after sanding (wet or dry)will do it but you'll probably be perued by the anti-terrorist guys if you try to buy it in sensible amounts these days, so thinners will probably do it anything that softens the old stuff.
Good luck.

your varnish manufacturer will have a de greaser. sand back the affected areas, treat and try again. could also be airborne pollution ie diesel car or truck nearby or if you have used wd40 or something with oils or solvents within a several mile radius!

Was the old varnish two pack as they may not "agree"??
Otherwise lots of preparation and final wipe with white spirit dampened cloth.

The general rule of thumb is that it's OK to put a one pack varnish on top of two pack (or an epoxy coat) but not the other way round.  So it looks like it's a silicone type problem you have there and yes it really is a bugger to get it all away.  One spot and you have this fish eyeing problem.  There are silicon sealer removers for bathrooms that you can get and I have wondered if they would be any good.

Definately sounds like a contaminated surface. A rub over with thinners should remove any grease/grime prior to varnishing. I remember once chatting to Laurie Smart at his yard when he had just finished rubbing down a surface ready for varnishing subsequently followed by me running my index finger along the surface commenting on how smooth it felt, how he didn't lamp me I don't know as Laurie had to spend more to time removing the grease deposited off my finger onto the surface. Golden rule number one ......never touch the surface prior to applying varnish.

funny enough I once touched a brand new helicopter at the factory with my finger and got into trouble for the 'greasy' finger mark.

I'll be trying some of the solutions today, so I'll report back!

Reporting back that the offending contaminant almost certainly silicone) was indeed removed by a scrub with thinners followed by some 180 grit sandpaper. Varnish went on no problem afterwards, thanks to all who contributed.

Haaving survived the silicone ordeal, I've then proceeded to inflict another body blow to my finishing!
I scrubbed the surface of another large area with thinners prior to a coat of epoxy - mindful of previous experience with silicone. This time the thinners itself was the culprit, resulting in what I now know are referred to as 'fisheyes'- little pits or voids in the epoxy (or varnish) finish.
It seems that in the lower temperatures, the thinners doesn't flash off as easily as it does on warmer days, and leaves a trace residue on the surface.  The organic nature of these prevents the epoxy (or varnish) from sticking.

Maybe the moral of the tale is to do this work in the summer. Definitely get the working environment up to above 15 - 18 degrees, and watch out for humidity% -  

Here is a useful web site for epoxy tips

This one summarised from the SP site - also helpful