Then I would guess your old magneto was timed slightly different.
That could be the explanation of the difference you are worried about.
The way I approach unexplained changes is by keeping spares and swapping them. Even if nothing changes, I might overhaul the original. I have a spare RSA fuel servo, a spare D3000 magneto, normally I have a spare alternator, two spare autopilot computers, a set of spare servos, a pile of spare avionics, etc. Crazy? For sure! But we are all crazy 
The basic issue is that a lot of faults will never be diagnosed, due to a lack of diagnostic capability / inadequate test procedures. And customer input on anything to specially check tends to be disregarded, either because the customer is assumed to be stupid or because their procedures don’t support it. So e.g. if you send a mag to a mag overhaul shop, telling them it makes a funny noise, they are unlikely to do anything different with it, to look for the noise. They will just throw it onto the mag tester, run it, if it passes it is tagged Serviceable and is by definition perfect.
This is one example. Never 100% for sure tracked down, but I demanded a different magneto returned to me after the overhaul 
This was another example which wasted a lot of my time, but at least was tracked down to a very visible crack. This article shows another aspect of it – a lot of avionics in the extended warranty swap pool are garbage, with intermittent faults.
If you don’t keep spares, it is much harder, because the same part will come back, probably with the same problem, and always tagged Serviceable. Often, this is a business where in the land of the blind the one eyed man is the king.
Raven and Peter, thank for your comments.
The possibilities you mention both may be very true. As said, it might have been a good idea to check the timing of the magneto’s before removal. On the other hand the “before overhaul” readings that I wish to see, have been there since new and the timing on 25 degrees has been checked on many yearly inspections.
However I indeed have the intention to remove the overhauled magneto again and bring it myself to the workshop and demand to be witnessing the testing and see what comes out. Comparing the both suggestions I think the timing issue will come the closest. During several test runs I also performed magneto checks in cruise (23 / 2330) and both magneto’s exactly showed the same behaviour (rise in EGT while keeping power setting the same).
Removing the Slick mag again may take a while as I have an potential buyer for the Lancair and this may be a third possible solution for the “problem”. Should this not work out then I will probably keep the Lancair thru the summer and I’m also considering to replace one Slick magnet by an electronic ignition such as the e-Mag. Any suggestions with regard to electronic ignitions? Especially while there is only very limited space within the Lancair cowling and it can be hot in there!
Regards,
Dave
By the way: Interesting stories about “weird problems and noises”. I have seen them quite a bit when I was marine engineer. The become even more weird when they resolve themselves. This happened to me (and again with EGT!! It seems to follow me) when I took-off some 10 years ago with the PH-DBO and saw the EGT climb over 1.500 F, while the full power figure normally was 1.400 F. I decided to return to the field, checked everything, found nothing and made no changes and took-off again. Guess what: everything normal again. I still think that I could have been taken-off on just one magneto although I normally very secure on procedures.
