I came across a situation I can't understand nor explain from what I know about reloading and I'd like your comments on this:

For my Mauser 30-06, 60 cm. barrel, bolt rifle I developed the following loads:
Hornady RN 150 gr. over 54 gr VV N150: 4 cm high at 100 meters.
Nosler Partition 200 gr. over 54 gr. VV N160:
dead on at 100 meters.
So two loads that shoot well in the same rifle; the 150 gr. bullets for lighter animals and the 200 grains for wild boar.

I also have a combo Blaser B95 in 12-70/30-06, also 60 cm. barrels
I worked up loads for this gun with the 150 gr. round noses and found 54 gr. VV N150 was as accurate as in my Mauser. (0.7-1.1 MOA for three shots) So I plan to stick to this load for both rifles. No chance of making mistakes and using the wrong cartridges

Then I tried the 200 gr. partitions over 53 gr. VV 160. Starting laod for this powder is 52,2 gr. and max is 57 gr. So this is a moderate load.
The 200 gr. partitions shoot about 20cm high at 100 meters compared tot the 150 gr. roundnoses
I sighted the Blaser in at 100 + 4 cm but at 50 metres the partitions shoot 3 cm. low.
The 150 gr. roundnoses now shoot about twenty cm low at 100 metres, as might be expected.

I know that every rifle is an individual and they all shoot different but I cannot think of any explanations for this enormous difference.

On the Mauser the scopeline is 3.5 cm. high and on the Blaser this is 7 cm, due to the fact that the upper barrel is a smooth 12 bore and the lower barrel is the rifle.

Who can elaboate on this?

Every gun barrel is a "tuning fork". The barrel is moving about slightly as the bullet exits the muzzle. (Hopefully, we the shooter will not add to that movement!). Certain loads may exit the barrel while it's in a upward node and others when in a downward node. It's possible for heavy bullets to be flicked upward and faster bullets to actually have a lower point of impact.
I'm not sure if I answered your question but these things can and do happen and it's all part of reloading. When everything makes perfect sense that darn "tuning fork" will throw a curve ball at you that doesn't make sense but there it is right in front of your eyes and you have to believe it.

There are a couple of other possible explanations:

1. The heavier bullet will not only exit the rifle more slowly but will also produce more recoil. This means the barrel will raise more from recoil before the heavier bullet exits the barrel.

2. Stock construction may be a factor. If there is more drop at the heel of the Blaser stock than in the Mauser, there would be, as it were a greater force moment around the rifles center of rotation with the heavier bullet. A stock, such as a varmint or bench rest stock with no drop at the heel will direct more of the force directly rearward (rather than upward) irrespective of the bullet weight.