Since the Remembering extension is from 2014-04-30, it’s from before I7 6L02 (three versions ago), so it’s possible that it has fallen out of sync with I7 as well as with Epistemology (it references v6, but the current version is 9).
Here’s one workaround for Mystery One; we want to consider only objects which were once seen but are not present at the moment, so we include this in our source:
Section - New Grammar Line (in place of Section - Grammar Line in Remembering by Aaron Reed)
Definition: A thing is absent if it is seen and it is not enclosed by the location of the player.
Understand
"examine [any absent thing]" or
"x [any absent thing]" or
"look at/for [any absent thing]" or
"take [any absent thing]" or
"get [any absent thing]" or
"pick up [any absent thing]" or
"pick [any absent thing] up" or
"drop [any absent thing]" or
"put down [any absent thing]" or
"put [any absent thing] down" or
"drop [any absent thing] away" or
"drop away [any absent thing]" or
"find [any absent thing]" or
"where is/are [any absent thing]" as remembering.
There are probably more elegant ways, which also address the other mysteries, but maybe it helps or can serve as a starting point. 
Edited to add two remarks:
-
for cross-reference, the problem was reported before (but apparently not solved): Remembering by Aaron Reed
-
test everything thoroughly, because the devil is in the details, as always… for example, I just found out that
>TAKE ALLcan result in problems, because if that action tries to take something, but then “remembers” it, it won’t continue taking the objects that are actually there: