As a pilot not an aircraft engineer.
On the encoding ones they have a vibrating thingy which is meant to reduce the lag in it. I suspect there is something up with that.
Reason.
If you had a leak in the static system the error would be pretty constant for a set attitude. And it would produce an error in your airspeed as well.
If it was water it would again give you a constant error.
You have 2 different types of Altimeter and we now have 2 aircraft without a fault on the basic altimeter but have one on the encoder.
The encoder does have a vibrator in it which by very nature is cyclic, you have a cyclic error.
Added in as well the mode C issues
Now the VSI giving you grief as well I haven't quite fitted in with my theory. But I suppose that what ever is driving the encoder is actually moving the bellows in it and I suppose it could be sending a back pressure down the tube. But with the lag in the VSI I wouldn't have expected it to register such a cyclic disturbance.
Personally as a none engineer I would get an avionics licensed type person to disconnect all the instruments on the static system and then block off all bar the last on the line and blow low pressure compressed air back through it (don't use an oxygen bottle it will have way to high a pressure on it). Then repeat for every outlet then go back to the first one again for a final squirt. If that doesn't fix it send your encoder off for service.
Or you could say sod it the Altimeter is a primary important bit of kit, its been in there for 15 years with nobody touching it. A service is small money in the grand scale of things and just do that first anyway.